RetrogeneDB ID: retro_pvam_973

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2008:45428..45914(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSPVAG00000010293
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_pvam_973
ACACCCAAAACAAGTGCGGCCCTCCAGGCACTGAAGCTCAAGAAGAGGTATGAAAAGCAGCTGGCACAGATGGATGCCAC
ACTATCGACCAGTAAGTTCCAGCAAGAGGCCCTGGAGAACGCCAACACCAACACCAACGTGCTCAAGAACACTGGCTATG
CTGCCAAAACTATGAAAGTTGCCGACGACAACATGGACATTGATAAAGCTGATGAGTTAATGCAGGACATTGCTGACCAG
CAAGAACTTGCAGAGATTTCAACAGCTATTTCAAAATCTCTAGGGTCTGCAGAAGACTTTGACGAGGGTAAGTTCATGGC
AGAATTAGAAGAATTAGAACAGGAGGGACTAGACAAGAATTTACTGGAAAAGAGTGGACCTGAAACAGGCCCTCTACCAA
ATGTTCTCTCTATTGCTCTACCATCAAAAGCCACCAAGAAGAAGGAAATCGACATGAAGGATTTGGAGTCCTGGGCTGGA
ACCATT

Alignment

ORF - retro_pvam_973 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.92 %
• Parental protein coverage: 74.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKNKRAALQALKRKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKV
          T....AALQALK.KKRYEKQLAQ.D.TLST..FQ.EALENANTNT.VLKN.GYAAK.MK.A.DNMDIDK.
Retrocopy TPKTSAALQALKLKKRYEKQLAQMDATLSTSKFQQEALENANTNTNVLKNTGYAAKTMKVADDNMDIDKA

Parental  DELMQDIADQQELAEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSIA
          DELMQDIADQQELAE.ISTAISK..G..E.FDE...MAELEELEQE.LDKNLLE.SGPET.PLPNV.SIA
Retrocopy DELMQDIADQQELAE-ISTAISKSLGSAEDFDEGKFMAELEELEQEGLDKNLLEKSGPETGPLPNVLSIA

Parental  LPSKPTKKKEEEDEDMKELESWAGTI
          LPSK.TKKKE....DMK.LESWAGTI
Retrocopy LPSKATKKKE---IDMKDLESWAGTI

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_973 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973 ,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,