Difference between revisions of "Lnc-NDFIP1-3:1"

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Please input one-sentence summary here.
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==Annotated Information==
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===Name===
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Approved name: SPRY4 intronic transcript 1 (non-protein coding)
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Alias: SPRY4-IT1
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LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0289259 HSALNT0289259]
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===Characteristics===
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Single exon ~700 nt transcript expressed in sense direction from the 2nd intron in SPRY4. Contains a SINE at 5' end. Secondary structure predicted to contain several long hairpins and multiple pseudoknots. 
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===Disease===
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melanoma
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===Function===
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Knockdown of SPRY4-IT1 in melanoma cells lines decreased cell viability, increased cell apoptosis. SPRY4-IT1 impacts cell invasion and cell mobility with decreased invasion and motility in SPRY4-IT1 knockdown cells and increased mobility (faster speed of migration) in SPRY4-IT1 over-expressing cell lines. 
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Conservation Not well conserved outside of primate, with 5' SINE element and predicted secondary structural elements only present in primates.
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===Expression===
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Expression significantly up-regulated in melanoma cell lines and patient tumour samples (both primary and metastatic) compared to melanocytes and keratinocytes. SPRY4-IT1 showed much greater expression variation across 20 human tissue than SPRY4. Both showed positively correlated expression and depending on the tissue either could be more highly expressed than the other. Knockdown of SPRY4-IT1 did not affect expression levels of SPRY4, validating that the two transcripts are independent. Localized predominately in the cytoplasm. Larger punctate nuclear signal could be transcription sites.
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===Conservation===
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Not well conserved outside of primate, with 5' SINE element and predicted secondary structural elements only present in primates.
 +
 
 +
===Misc===
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SPRY4 protein coding gene is also more highly expressed in melanoma cells and patient samples compared to melanocytes. It is unclear if SPRY4-IT1 has a separate promoter or is transcribed as part of the SPRY4 transcript.
  
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==Annotated Information==
 
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
 
Please input transcriptomic nomeclature information here.
 
Please input transcriptomic nomeclature information here.
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===Function===
 
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Please input function information here.
 
  
 
===Regulation===
 
===Regulation===
 
Please input regulation information here.
 
Please input regulation information here.
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===Expression===
 
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Please input expression information here.
 
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
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==References==
 
==References==
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Please input cited references here.
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[http://www.lncrnadb.org/spry4-it1/ Annotaion originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>GTAGAGATGGGGGTTTCATCCTGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATCTGCCTACCTTGGCCTCCCAAAAGGCTGAGATTACAGGCATGAGCCACTGCGCCAGGCCTTCTTTCTTTTCTTTTTTTCTTTCTTTTTTTTTTTTGAGACATCATTTAGCTGTGCTGAGGGGTTCTTAAATAGGCAGCTCAGAAAATTGTTTTCCTTTGTCAGCCACATAAATTCAGCAGAGGCTCTTGGAGGGTCCCTGCTGGTGAGGGGTGAGGCCAGCAGTGGAACTCTGATTTGGTTTTTGCTGAGCTGGTGGTTGAAAGGAATCCTACTACATCGGGGTTATAATAGGGAAGATACATTTTAGAATATGCCCAGTGGAGCCATCGGATGCTGCATCGTCCCCAGAGAGCCAAGTCATCGTGGGCCAAGCTCCCATCCCCATGTCTGGCCTCAACTGCAGGCCCAGAATGTTGACAGCTGCCTCTTGGAGGGTTATGGGAGCCTGTGAATGCCAACATCCCCATTTGCCTGCAGCGGCTGCTCCCATCCTGGCTTCCTGGTGGGACTTTTCCATGAATTGGGGAATCTGCTTTCTGATTCCAAGGCCTATTAAAATTTCTGAGCATTGCCCATTTCTTTTGCTTTATCTGTAGGACATGGGCTGTTTTTAAAGAACCTCACAAATGAAAAAAAAAAAAAAAAA</dnaseq>|
 
sequence = <dnaseq>GTAGAGATGGGGGTTTCATCCTGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATCTGCCTACCTTGGCCTCCCAAAAGGCTGAGATTACAGGCATGAGCCACTGCGCCAGGCCTTCTTTCTTTTCTTTTTTTCTTTCTTTTTTTTTTTTGAGACATCATTTAGCTGTGCTGAGGGGTTCTTAAATAGGCAGCTCAGAAAATTGTTTTCCTTTGTCAGCCACATAAATTCAGCAGAGGCTCTTGGAGGGTCCCTGCTGGTGAGGGGTGAGGCCAGCAGTGGAACTCTGATTTGGTTTTTGCTGAGCTGGTGGTTGAAAGGAATCCTACTACATCGGGGTTATAATAGGGAAGATACATTTTAGAATATGCCCAGTGGAGCCATCGGATGCTGCATCGTCCCCAGAGAGCCAAGTCATCGTGGGCCAAGCTCCCATCCCCATGTCTGGCCTCAACTGCAGGCCCAGAATGTTGACAGCTGCCTCTTGGAGGGTTATGGGAGCCTGTGAATGCCAACATCCCCATTTGCCTGCAGCGGCTGCTCCCATCCTGGCTTCCTGGTGGGACTTTTCCATGAATTGGGGAATCTGCTTTCTGATTCCAAGGCCTATTAAAATTTCTGAGCATTGCCCATTTCTTTTGCTTTATCTGTAGGACATGGGCTGTTTTTAAAGAACCTCACAAATGAAAAAAAAAAAAAAAAA</dnaseq>|
 
}}
 
}}
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[[Category:Intronic(AS)]]
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[[Category:Intronic(AS)]][[Category:Transcripts]]
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{{lncrnadb|
 
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tID = lnc-NDFIP1-3:1|
 
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ltID = SPRY4-IT1|
 
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ann = <tab class=wikitable sep=tab head=top>
 
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Section Description
 
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ID SPRY4-IT1
 
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Characteristics Single exon ~700 nt transcript expressed in sense direction from the 2nd intron in SPRY4. Contains a SINE at 5' end. Secondary structure predicted to contain several long hairpins and multiple pseudoknots. 
 
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Expression Expression significantly up-regulated in melanoma cell lines and patient tumour samples (both primary and metastatic) compared to melanocytes and keratinocytes. SPRY4-IT1 showed much greater expression variation across 20 human tissue than SPRY4. Both showed positively correlated expression and depending on the tissue either could be more highly expressed than the other. Knockdown of SPRY4-IT1 did not affect expression levels of SPRY4, validating that the two transcripts are independent. Localized predominately in the cytoplasm. Larger punctate nuclear signal could be transcription sites.
 
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Function Knockdown of SPRY4-IT1 in melanoma cells lines decreased cell viability, increased cell apoptosis. SPRY4-IT1 impacts cell invasion and cell mobility with decreased invasion and motility in SPRY4-IT1 knockdown cells and increased mobility (faster speed of migration) in SPRY4-IT1 over-expressing cell lines. 
 
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Conservation Not well conserved outside of primate, with 5' SINE element and predicted secondary structural elements only present in primates.
 
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Misc SPRY4 protein coding gene is also more highly expressed in melanoma cells and patient samples compared to melanocytes. It is unclear if SPRY4-IT1 has a separate promoter or is transcribed as part of the SPRY4 transcript.
 
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Name SPRY4 intronic transcript 1 (non-protein coding)
 
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</tab>|
 
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}}
 

Latest revision as of 10:59, 21 August 2019

Annotated Information

Name

Approved name: SPRY4 intronic transcript 1 (non-protein coding)

Alias: SPRY4-IT1

LncBook ID: HSALNT0289259

Characteristics

Single exon ~700 nt transcript expressed in sense direction from the 2nd intron in SPRY4. Contains a SINE at 5' end. Secondary structure predicted to contain several long hairpins and multiple pseudoknots.

Disease

melanoma

Function

Knockdown of SPRY4-IT1 in melanoma cells lines decreased cell viability, increased cell apoptosis. SPRY4-IT1 impacts cell invasion and cell mobility with decreased invasion and motility in SPRY4-IT1 knockdown cells and increased mobility (faster speed of migration) in SPRY4-IT1 over-expressing cell lines. Conservation Not well conserved outside of primate, with 5' SINE element and predicted secondary structural elements only present in primates.

Expression

Expression significantly up-regulated in melanoma cell lines and patient tumour samples (both primary and metastatic) compared to melanocytes and keratinocytes. SPRY4-IT1 showed much greater expression variation across 20 human tissue than SPRY4. Both showed positively correlated expression and depending on the tissue either could be more highly expressed than the other. Knockdown of SPRY4-IT1 did not affect expression levels of SPRY4, validating that the two transcripts are independent. Localized predominately in the cytoplasm. Larger punctate nuclear signal could be transcription sites.

Conservation

Not well conserved outside of primate, with 5' SINE element and predicted secondary structural elements only present in primates.

Misc

SPRY4 protein coding gene is also more highly expressed in melanoma cells and patient samples compared to melanocytes. It is unclear if SPRY4-IT1 has a separate promoter or is transcribed as part of the SPRY4 transcript.

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Regulation

Please input regulation information here.

Allelic Information and Variation

Please input allelic information and variation information here.

Evolution

Please input evolution information here.

You can also add sub-section(s) at will.

Labs working on this lncRNA

Please input related labs here.

References

Annotaion originally sourced from lncRNAdb.

Basic Information

Transcript ID

lnc-NDFIP1-3:1

Source

LNCipedia2.1

Same with

,

Classification

intronic(AS)

Length

708 nt

Genomic location

chr5+:141697198..141697887

Exon number

,

Exons

,

Genome context

Sequence
000001 GTAGAGATGG GGGTTTCATC CTGTTGGTCA GGCTGGTCTT GAACTCCTGA CCTCAAGTGA TCTGCCTACC TTGGCCTCCC 000080
000081 AAAAGGCTGA GATTACAGGC ATGAGCCACT GCGCCAGGCC TTCTTTCTTT TCTTTTTTTC TTTCTTTTTT TTTTTTGAGA 000160
000161 CATCATTTAG CTGTGCTGAG GGGTTCTTAA ATAGGCAGCT CAGAAAATTG TTTTCCTTTG TCAGCCACAT AAATTCAGCA 000240
000241 GAGGCTCTTG GAGGGTCCCT GCTGGTGAGG GGTGAGGCCA GCAGTGGAAC TCTGATTTGG TTTTTGCTGA GCTGGTGGTT 000320
000321 GAAAGGAATC CTACTACATC GGGGTTATAA TAGGGAAGAT ACATTTTAGA ATATGCCCAG TGGAGCCATC GGATGCTGCA 000400
000401 TCGTCCCCAG AGAGCCAAGT CATCGTGGGC CAAGCTCCCA TCCCCATGTC TGGCCTCAAC TGCAGGCCCA GAATGTTGAC 000480
000481 AGCTGCCTCT TGGAGGGTTA TGGGAGCCTG TGAATGCCAA CATCCCCATT TGCCTGCAGC GGCTGCTCCC ATCCTGGCTT 000560
000561 CCTGGTGGGA CTTTTCCATG AATTGGGGAA TCTGCTTTCT GATTCCAAGG CCTATTAAAA TTTCTGAGCA TTGCCCATTT 000640
000641 CTTTTGCTTT ATCTGTAGGA CATGGGCTGT TTTTAAAGAA CCTCACAAAT GAAAAAAAAA AAAAAAAA
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