RetrogeneDB ID: retro_pvam_901

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_15817:26397..27086(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CLIC5
• Ensembl ID: ENSPVAG00000006075
• Aliases: None
• Description: chloride intracellular channel 5 [Source:HGNC Symbol;Acc:13517]

Sequence

>retro_pvam_901
CTCTTCGTCAAGGCTGGCAGTGATGGTAAAAGCCTAGGAAACTGCCCCTTTTCCCAGGCACTCTTCATGATTCTTTAGCT
CAAAGAAGTTGTATTTAGTGTTGCTACCATGGACCTGAAAAGAAAGCCTGTAGATCTGCAGAGCTTGACTACTGGGACCC
ACCCATCATTTATAACTTACAACGATGAAGTCAAAACGGATGTAAATAAGACTGAAGAATTTCTTGAAGGAGGCATATGC
CCTCCCAAGTACTTAAAAGCTTTCATCGAAATACTCAGAATTGAATAATGCTGGAATGGACATCTTTGCCAAATTTTCTG
CATATATTAAGAATTCAAGACCAGAGGCTAATGAAGCATTGGAGAGGGACCTCTTGAAAACACTACAGAAACTGGATAAA
TATCTGATTTCTCCCCTCCCTGATGAAATTGCTGAGAATAGTATGGGAAATGCTACAAGTTTTCCACACGTAAATTTCTG
GATGGTAATGAAATGACATGGCTAATTGCAACCTGCTGCCCAAACTGCACATTGTCAAGGTGGTGGCCAAAAAATATCAC
AACTTTGATATTCCAAAAGCATGACTGGCCATCTGTAGATACTTAACTAATGCTTATAGTAGGGATGAGTTCACAAATAC
CTGTCCCAGTGATAAGGAGGTTGAAATAGCGTATAGTGATGTAACCAAG

Alignment

ORF - retro_pvam_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.52 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFVKAGIDGESIGNCPFSQRLFMILWLKGVVFNVTTVDLKRKPADLHNLAPGTHPPFLTFNGDVKTDVNK
          LFVKAG.DG.S.GNCPFSQ.LFMIL.LK.VVF.V.T.DLKRKP.DL..L..GTHP.F.T.N..VKTDVNK
Retrocopy LFVKAGSDGKSLGNCPFSQALFMIL*LKEVVFSVATMDLKRKPVDLQSLTTGTHPSFITYNDEVKTDVNK

Parental  IEEFLEETLTPEKYP-RLAAKHRGSNTAGIDIFSKFSAYIKNTKQQNNAALERGLTKALKELDDYLNTPL
          .EEFLE....P.KY...L..K....N.AG.DIF.KFSAYIKN.....N.ALER.L.K.L..LD.YL..PL
Retrocopy TEEFLEGGICPPKYL>KLSSKYSELNNAGMDIFAKFSAYIKNSRPEANEALERDLLKTLQKLDKYLISPL

Parental  PEEIDANTHGDDD-KRSRRKFLDGDELT-LADCNLLPKLHVVQIVSRKYRNYNFPAEMTGLWRYLKNAYA
          P.EI..N..G....K.S.RKFLDG.E.T..A.CNLLPKLH.V..V..KY.N...P.......RYL.NAY.
Retrocopy PDEIAENSMGNAT<KFSTRKFLDGNEMT<MANCNLLPKLHIVKVVAKKYHNFDIPKA*LAICRYLTNAYS

Parental  RDEFTNTCAADSEIELAYADVAK
          RDEFTNTC..D.E.E.AY.DV.K
Retrocopy RDEFTNTCPSDKEVEIAYSDVTK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_901 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Pteropus vampyrus	ENSPVAG00000006075	1 retrocopy	retro_pvam_901 ,
Tupaia belangeri	ENSTBEG00000007344	1 retrocopy	retro_tbel_2021,