RetrogeneDB ID: retro_ggor_1393

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:1342458..1343159(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000009010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSGGOG00000026651
• Aliases: None
• Description: None

Sequence

>retro_ggor_1393
GTAGACCCTCTTAATATGCATGTTACTTGGAAGTGATATAGCAGGTTTAGATGAGGTCATTACGGATCTGAAAGACAGTC
ATCTTACCTATCAAAAAGAAACATTTGTTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGGTGTTCTTCTCTATGAGCC
TCCCCAGGCTGTGGTAAAACGTTGATTGCCAAGGCCACAGCCAAAGAAGCAGGCTGTCGATTTATTAACCTTGAGCCTTC
GACACTGACCAATAAGTGGTATGGAGAATCTCAAACACTGGCTGCTGCTGTCTTCTCCCTTGCCATAAAGCTACAACTGT
CCATCATCATTATAGACGAAATAGACTCCTTTCTACGAAACCGTTCGGAGTTCTGACCATGAAGCTACAGCCATAATGAA
AGCTCAGTTTATGAGTCTGTGGGATGGACTGGATACTGATCACAGCTGCCAGGTCATAGTAATGGGAGCTACCATTCATC
CTCAGGACCTTGACACGGCTATAACGAGAAGAATTCCTACAAGATTTCATATCAACCAGCCTGCTTTAAAACAGAAAGAA
GCAATCCTGAAACTCATCTTGAAAAATGAAAATGTGGATTGGCATGTAGACCTGCTAGAAGTTGCCCGGGAAACTGATGC
GTTTTCAGGAAGGGACCTAAATGCGATGTGTTGAGATGCTGCCCTCCTCTGTGTTAGAGAA

Alignment

ORF - retro_ggor_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 63.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDPLNMHVTW-SDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKE
          VDPLNMHVTW.SDIAGLD.VITDLKD......K.....E............L...PGCGKTLIAKATAKE
Retrocopy VDPLNMHVTW>SDIAGLDEVITDLKDSHLTYQKETFV*EFQASAASKRCSSL*ASPGCGKTLIAKATAKE

Parental  AGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRS-SSDHEATAMMKAQFMS
          AGCRFINL.PSTLT.KWYGESQ.LAAAVFSLAIKLQ.SII.IDEIDSFLRNRS.SSDHEATA.MKAQFMS
Retrocopy AGCRFINLEPSTLTNKWYGESQTLAAAVFSLAIKLQLSIIIIDEIDSFLRNRS>SSDHEATAIMKAQFMS

Parental  LWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPVARHQNTFLKICLHKKSVDRHVDLLEVA
          LWDGLDTDHSCQVIVMGAT..PQDLD.AI.RR.PTRFHINQP........LK..L....VD.HVDLLEVA
Retrocopy LWDGLDTDHSCQVIVMGATIHPQDLDTAITRRIPTRFHINQPALKQKEAILKLILKNENVDWHVDLLEVA

Parental  QETDGFSGSDLKEMCRDAALLCVRE
          .ETD.FSG.DL..MC.DAALLCVRE
Retrocopy RETDAFSGRDLNAMC*DAALLCVRE

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	1.39 RPM	28.34 RPM
SRP007412_cerebellum	0.67 RPM	19.62 RPM
SRP007412_heart	0.34 RPM	6.04 RPM
SRP007412_kidney	1.23 RPM	23.35 RPM
SRP007412_liver	0.82 RPM	16.12 RPM
SRP007412_testis	9.01 RPM	136.44 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_1393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1393 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1900
Pan troglodytes	retro_ptro_1255
Callithrix jacchus	retro_cjac_1101

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393 ,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,