RetrogeneDB ID: retro_ptro_915

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:54272640..54273257(+)
• Located in intron of: ENSPTRG00000006373

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSPTRG00000013408
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_ptro_915
GCTGGAGGGGGTAAGGCCAGCAAGGGCGGCCCGACCCTCCAGGAGGCCATCCAGCGGCTGCGGGACACGGAGGAGATGTT
AAGCAAGAAACAGGAGTTCCTGGAGAAGAAAATCGAGCAGAGGCACGGCACCAAAAACAAGGGCGCGGCCCTCCAGGCAC
TGAAGCGTAAGAAGAGGTATGAGAAGCAGCTGGCGCAGATCGACGGCACATTATCAACCATCGAGTTCCAGCAGCAGGCT
CTGGAGAACGCCAACACCAATACCGAGGTGCTCAAGAACATGGGCTCTGCCGCCAAGGCCAAGAAGGCGGCCCACGACAA
CATGGACATCGATAAAGTTGATGAGTTAATGCAGGACATTGCTGACCAACAAGAACTTGAGGAGGAGATTTCAACAGCAA
TTTCTAAACCTGTAGGGTTTGGAGAAAAGTCTGACGAGGATGAGCTCATGGCGGAATTAGAAGAACTAGAACAGGAGCAA
CCAGACAAGAATTTGCTGGAAATCAGTGGCCCCGAAACAGTCCTTCTACCAAATGTTCCCTCTATAGCCCTACCATCAAA
ACCTGCCAAGAAGAGGAAGACGACGACATGAAGGATTTGGAGAACTGGGCTGGGTCC

Alignment

ORF - retro_ptro_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 93.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGKGGPPQEAIQLRDTEEMLSKKQEFLEKKIE-QELTAAKKHGTKHKRAALQALKRKKRYEKQLAQIDGT
          AG.G........L......L....E.L.KK.E..E......HGTK.K.AALQALKRKKRYEKQLAQIDGT
Retrocopy AGGGKASKGGPTLQEAIQRLRDTEEMLSKKQEFLEKKIEQRHGTKNKGAALQALKRKKRYEKQLAQIDGT

Parental  LSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQELAEEISTAISKPVGF
          LSTIEFQ..ALENANTNTEVLKNMG.AAKA.KAAHDNMDIDKVDELMQDIADQQEL.EEISTAISKPVGF
Retrocopy LSTIEFQQQALENANTNTEVLKNMGSAAKAKKAAHDNMDIDKVDELMQDIADQQELEEEISTAISKPVGF

Parental  GEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSIALPSKPAKKK-EEEDDDMKELENWAGS
          GE..DEDELMAELEELEQE..DKNLLEISGPETV.LPNVPSIALPSKPAKK..E..D..MK.LENWAGS
Retrocopy GEKSDEDELMAELEELEQEQPDKNLLEISGPETVLLPNVPSIALPSKPAKKR<EDDD--MKDLENWAGS

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.82 RPM	166.68 RPM
SRP007412_cerebellum	1.25 RPM	118.12 RPM
SRP007412_heart	0.79 RPM	81.35 RPM
SRP007412_kidney	2.48 RPM	116.19 RPM
SRP007412_liver	2.55 RPM	146.13 RPM
SRP007412_testis	1.58 RPM	67.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_915 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_915 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1339
Pongo abelii	retro_pabe_1111

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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,