RetrogeneDB ID: retro_ptro_599

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:34319378..34319895(-)
• Located in intron of: ENSPTRG00000003495

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSPTRG00000012525
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]

Sequence

>retro_ptro_599
TCTCATGTGGCCGCTCTACCTCCAGATATATGCTCTCAAAAGGTGTGGCCTGATGAAACTATGGGACCGTTTGGACCTCA
AGATCAGAGGTTCAAGCTTCCTGGGATCATAGGTTTTGATTGTCACCTCAATGGGACTGCTTCACAGAAGAAAAGCCTGC
TTTATAAAACTTTGCCTGATGTTCTAGCAGAAACTTTATCAAGTGAAAGACACAAGTTTGTGATGACACAATATGTGAGT
GAATTTCAGGGTAATGATGCACCTGTTGAACAAGAAATTAACAGTGCAGAAACTTAACTTTGAAAGTGCCAGAGTGGAGT
GTGCAATACAAACGTGTCCAGAATTGCGGCGAAAAGATTTTGAATCACTGTTTCCAGAAGTAGCTAATAGCAAATTAATC
ATTCTGATTGTAACACAGAAAACTAAGAATAATATGACTGTTTAGAGTGAAGAAGTAGAAACTGAAAGAGAAGTGCTCTT
AGAAAAGTTCATCAATGTTGCTAAGGAAATTTGCTGT

Alignment

ORF - retro_ptro_599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHVAAAPPDICSRTVWPDETMGPFGPQDQRFQLPGNIGFDCHLNGTASQKKSLVHKTLPDVLAEPLSSER
          SHVAA.PPDICS..VWPDETMGPFGPQDQRF.LPG.IGFDCHLNGTASQKKSL..KTLPDVLAE.LSSER
Retrocopy SHVAALPPDICSQKVWPDETMGPFGPQDQRFKLPGIIGFDCHLNGTASQKKSLLYKTLPDVLAETLSSER

Parental  HEFVMAQYVNEFQGNDAPVEQEINSAET-YFESARVECAIQTCPELLRKDFESLFPEVANGKLMILTVTQ
          H.FVM.QYV.EFQGNDAPVEQEINSAET..FESARVECAIQTCPEL.RKDFESLFPEVAN.KL.IL.VTQ
Retrocopy HKFVMTQYVSEFQGNDAPVEQEINSAET>NFESARVECAIQTCPELRRKDFESLFPEVANSKLIILIVTQ

Parental  KTKNDMTVWSEEVEIEREVLLEKTESLSPRPECC
          KTKN.MTV.SEEVE.EREVLLEK.........CC
Retrocopy KTKNNMTV*SEEVETEREVLLEKFINVA-KEICC

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	0.04 RPM	20.29 RPM
SRP007412_cerebellum	0.04 RPM	18.46 RPM
SRP007412_heart	0.26 RPM	35.91 RPM
SRP007412_kidney	0.13 RPM	37.21 RPM
SRP007412_liver	0.16 RPM	31.36 RPM
SRP007412_testis	0.11 RPM	79.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_599 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_599 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_865
Gorilla gorilla	retro_ggor_704
Macaca mulatta	retro_mmul_1058

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716, retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749, retro_mdom_620,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599 ,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,