Lnc-NDFIP1-3:1

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Annotated Information

Name

SPRY4 intronic transcript 1 (non-protein coding)

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.

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

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Regulation

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Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

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References

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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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