RetrogeneDB ID: retro_ggor_704

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:34901298..34902064(-)
• Located in intron of: ENSGGOG00000014588

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSGGOG00000027348
• Aliases: None
• Description: None

Sequence

>retro_ggor_704
TCTCATGTGGCCAGTCTACCTCCAGATATATGCTCTCAAACGGTATGGCCTGATGAAACTGTGGGACCGTTTGGACCTCA
AGATCAGAGGTTCAAGCTTCCTGGGATCATAGGTTTTGATTGTCACCTCAATGGGACTGCTTCACAGAAGAAAAGCCTGC
TTTATAAAACTTTGCCTGATGTTCTAGCAGAAACTTTATCAAGTGAAAGACACGAGTTTGTGATGACACAATATGTGAAT
GAATTTCAGGGTAATGATGCACCTGTTGAACAAGAAATTAACAGTGCAGAAACTTAACTTTGAAAGTGCCAGAGTGGAGT
GTGCAATACAAACGTGTCCAGAATTGTGGCGAAAAGATTTTGAATCACTGTTTCCAGAAGTAGCTAATAGCAAACTAATC
ATTCTGACTGTAACACAGAAAACTAAGAATAATATGACTCTTTAGAGTGAAGAAGTAGAAACTGAAAGAGAAGTGCTCTT
AGAAAAGTTCATCAATGGTGCTAAGGAAATTTGCTGTGCTCTTTGAGCTGAGAGATATTGGGCTGACTTTACTGACCCAT
TATCTGGTTTGGCATTTTTTTGGACCATATACAAACAACACTCTTTTTGAAACTGATGAATGCTACCGACATTTAGGATT
CTCTGTTGATGACCTTCGATGCTTAAAGTGATTCGTCATAGTCTCTGGGGTACCCGTGTAGTTGTAGGAAGCATCTTCAC
TAATGCAACACCAGACAGCCATATTATGAAGAAATTAAGTGGAAAT

Alignment

ORF - retro_ggor_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SHVAAAPPDICSRTVWPDETMGPFGPQDQRFQLPGNIGFDCHLNGTASQKKSLVHKTLPDVLAEPLSSER
          SHVA..PPDICS.TVWPDET.GPFGPQDQRF.LPG.IGFDCHLNGTASQKKSL..KTLPDVLAE.LSSER
Retrocopy SHVASLPPDICSQTVWPDETVGPFGPQDQRFKLPGIIGFDCHLNGTASQKKSLLYKTLPDVLAETLSSER

Parental  HEFVMAQYVNEFQGNDAPVEQEINSAET-YFESARVECAIQTCPELLRKDFESLFPEVANGKLMILTVTQ
          HEFVM.QYVNEFQGNDAPVEQEINSAET..FESARVECAIQTCPEL.RKDFESLFPEVAN.KL.ILTVTQ
Retrocopy HEFVMTQYVNEFQGNDAPVEQEINSAET>NFESARVECAIQTCPELWRKDFESLFPEVANSKLIILTVTQ

Parental  KTKNDMTVWSEEVEIEREVLLEKFINGAKEICYALRAEGYWADFIDPSSGLA-FFGPYTNNTLFETDERY
          KTKN.MT..SEEVE.EREVLLEKFINGAKEIC.AL.AE.YWADF.DP.SGLA.FFGPYTNNTLFETDE.Y
Retrocopy KTKNNMTL*SEEVETEREVLLEKFINGAKEICCAL*AERYWADFTDPLSGLA>FFGPYTNNTLFETDECY

Parental  RHLGFSVDDLGC-CKVIRHSLWGTHVVVGSIFTNATPDSHIMKKLSGN
          RHLGFSVDDL.C..KVIRHSLWGT.VVVGSIFTNATPDSHIMKKLSGN
Retrocopy RHLGFSVDDLRC<LKVIRHSLWGTRVVVGSIFTNATPDSHIMKKLSGN

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	0.05 RPM	21.34 RPM
SRP007412_cerebellum	0.04 RPM	19.07 RPM
SRP007412_heart	0.00 RPM	11.26 RPM
SRP007412_kidney	0.04 RPM	45.75 RPM
SRP007412_liver	0.03 RPM	55.13 RPM
SRP007412_testis	0.00 RPM	77.08 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_704 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_865
Pan troglodytes	retro_ptro_599
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,