RetrogeneDB ID: retro_pvam_15

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_15006:5088..5994(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000004069
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000010393
• Aliases: None
• Description: None

Sequence

>retro_pvam_15
ATGAAGTCCAACCCTGTCATCCAAGCCGCCATCGACCTCACAGCGGGGGCCCTCGGGGGCACCGCGTGTGTCCTGACCGG
GCAGCCCTTCGACACAGTGAAAGTGAAGATGCAGACGTTCCCTGCCCTGTACAAGGGCTTCACCGACTGCTGCCTGAAGA
CATACTCCCAAGTGGGCTTGCGCGGCTTCTACAAGGGGACCGGTCCGGCGCTGATGGCCTACGTCGCCGAGAACTCTGTC
CTCTTCATGTGCTACGGCTTCTGCCAACAGTTTGTGAAGAAAGTAGTGGGACTGGACAAGCAGGCAAAGCTGAGTGATCT
GCAGACTGCAACTGCCGGTTCCTTAGCCTCTGGGTTTGCTGCGCTGGCCCTGTGTCCCACTGAGCTTGTGAAGTGCCGAC
TACAGACCATGCACGAAATGGAGATGTCAGGGAAGATAGCCAAAAGCCACAATACAGTTTGGTCCGTCATGAAGGGTATC
CTTAGGAAGGATGGCCCCTTGGGCTTCTACCACGGACTCTCGAGTACTCTACTTCAAGAAGTACCAGGCTATTTCTTCTT
CTTTGGTGGCTATGAACTGAGCAGATCATTTTTTGCCTCAGGGAGATCAAAAGATGAACTAGGCCCTGTCTCTTTGATGT
TAAGTGGTGGAATTGCTGGGATTTGCCTTTGGCTTGTCATATTCCCAGTGGATTGTATCAAATCCAGAATTCAGGTTCTT
TCCATGTCTGGAAAACAGGCAGGATTTATCGGGACTCTTTTAAGTATTGTGGAAAGTGAAGGAATAACAGCCTTATATTC
TGGACTGACAGCTACTATGATTCGAGCGTTCCCTGCTAATGGGTCACTGTTTTTGGCTTATGAATACAGTAGGAAGATGA
TGATGAGGCAGTTAGATGCATACTAA

Alignment

ORF - retro_pvam_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEMETSGKIAKSQNTVWSVVKSILRKDGPLGFYRGLSS
          DLQ.A.AGS.AS.FAAL.LCPTELVKCRLQTM.EME.SGKIAKS.NTVWSV.K.ILRKDGPLGFY.GLSS
Retrocopy DLQTATAGSLASGFAALALCPTELVKCRLQTMHEMEMSGKIAKSHNTVWSVMKGILRKDGPLGFYHGLSS

Parental  TLLREVPGYFFFFGGYELSRSFFASGRSKDELGPVSLMLSGGVGGICLWLAVYPVDCIKSRIQVLSMSGK
          TLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPVSLMLSGG..GICLWL...PVDCIKSRIQVLSMSGK
Retrocopy TLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPVSLMLSGGIAGICLWLVIFPVDCIKSRIQVLSMSGK

Parental  QTGFIGTFISVMKNEGIMALYSGLKPTIIRAFPANGSLFLAYEYSRKLMMSQFEAH
          Q.GFIGT..S....EGI.ALYSGL..T.IRAFPANGSLFLAYEYSRK.MM.Q..A.
Retrocopy QAGFIGTLLSIVESEGITALYSGLTATMIRAFPANGSLFLAYEYSRKMMMRQLDAY

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_15 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15 ,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,