RetrogeneDB ID: retro_pvam_942

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1805:106017..106601(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX15
• Ensembl ID: ENSPVAG00000007902
• Aliases: None
• Description: sorting nexin 15 [Source:HGNC Symbol;Acc:14978]

Sequence

>retro_pvam_942
CCATCCCCAGATGAGCCCTGGCCACCTCCTGATGAGCTCTGGTTTACCTGCCTCTCCCTGTGGAAAGGAGAGGCCTTCAG
GAGCTGGAGGTGCCATGGACCTCGCCATCCAGCCCTGCCGGGAGGTCCTAGATCTCCTCTGAAACTGTGAGAGCACCAGG
AGGGGTCCTGCCAAAGACCCCTCTCTGAGGCTGAGCTTACCCTCTTCATCCCTTCTCCAAGGAAACAGGTGCAGGCCCAG
TCCCACCCACATAGGCGAGCGGGCCGTGATGCAGGCAGAGTCCTAAAGGCTGGACCAGAAACCTTGGGAGCTGAGAAGGC
AGGAGGAGGTAGAGGTCAAGAGGATGGAGGGCTTGCCCCTGCCTCTCTGAGCTGCGCCAAAGAGCTCATCGCCCAGGCCC
TGAAAGAGGAGGAGGCAGGTGCCTACCCTGTGGCTCTGCAGGGCCGGGGGACTACCACACACCCTGCTTCAGGGGGTCCC
AGTGACACGTCTCCTGCCTTCAGGGAGGTGTGAAGAAGGAGGCAGCTGAGCACTTGAAGTGGGCAGACGCAATCCGGCTC
CTGCCCTTCTCCCGGCCCCCACCC

Alignment

ORF - retro_pvam_942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.42 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PPPLIPTPPPDESWLP-QPLPVEKRGLEESEVPADPPPSSPA-QEALDLLFNGGSTEEASGSPARGP-LT
          P.P..P.PPPDE.W....PLPVE.RGL.E.EVP...P.SSPA..E.LDLL.N..ST......PA..P.L.
Retrocopy PSPDEPWPPPDELWFT<LPLPVERRGLQELEVPWTSP-SSPA<REVLDLL*NCESTRRG---PAKDP<LS

Parental  EAELALF-DPFSREEGAG-PSPTHIGELAAMEAESERPDQEPWEPGGQEEEEDK-EGGS-TPAYLSQATE
          EAEL.LF..PFS.E.GAG.PSPTHIGE.A.M.AES.R.DQ.PWE...QEE.E.K.E.G...PA.LS.A.E
Retrocopy EAELTLF<HPFSKETGAG<PSPTHIGERAVMQAES*RLDQKPWELRRQEEVEVK<EDGGLAPASLSCAKE

Parental  LITQALRDEKAGAYPAALQGYRDGVHILLQGVPGDPSPARQE-GVKKKAAAYLKRAEEILHLHLSQLPP
          LI.QAL..E.AGAYP.ALQG.....H....G.P.D.SPA..E.GVKK.AA..LK.A..I..L..S..PP
Retrocopy LIAQALKEEEAGAYPVALQGRGTTTH-PASGGPSDTSPAFRE<GVKKEAAEHLKWADAIRLLPFSRPPP

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_942 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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000007902	1 retrocopy	retro_pvam_942 ,
Tursiops truncatus	ENSTTRG00000000324	1 retrocopy	retro_ttru_378,