RetrogeneDB ID: retro_ggor_1731

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:67888710..67889132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022675
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSGGOG00000005285
• Aliases: None
• Description: None

Sequence

>retro_ggor_1731
ATGTCACACATGCTCCTGCACCTCCACAGCAGCTGGCAAGTGGACCAGGCCATCCTCCCAGGAGAGGACTGCATGGTTGT
CATTTGCTTCGGCCACGACTGGGACCCCACATGCATGAAAATGGACAAGGTCTTGTACAGCATCATTGAGAAGGTTAAAG
ATTTTGCAGTTATTTTTCTTGTGGATATTACCAAAGTACCTAACTTCAACAAAATGTATGAGTTATATGATCCATGCACT
ATCATGTTTTTCTTCAGGAACAAGCACATCATGGTTGTCTTGGGGACTGGCAACAACAAGATTAACTGGGCCATGGAGGA
CAAGCAGGAGATGGTCGACATCATAGAGACCGTGGACTGTAGGGCCCTCAATGGTGACGACCTGGTATTGTCCCCAAAAA
CTACTCCACCAAGTCCAGATAC

Alignment

ORF - retro_ggor_1731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFN
          MS.ML.HLH..WQVDQAIL..ED..VVI.FGHDWDPTCMKMD.VLYSI.EKVK.FAVI.LVDIT.VP.FN
Retrocopy MSHMLLHLHSSWQVDQAILPGEDCMVVICFGHDWDPTCMKMDKVLYSIIEKVKDFAVIFLVDITKVPNFN

Parental  KMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVS-PKDYSTK
          KMYELYDPCT.MFFFRNKHIM..LGTG.NNKINWAMEDKQEMVDIIETV...A..G..LV.S.PK.YSTK
Retrocopy KMYELYDPCTIMFFFRNKHIMVVLGTG-NNKINWAMEDKQEMVDIIETVDCRALNGDDLVLS<PKNYSTK

Parental  YRY
          .RY
Retrocopy SRY

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	0.00 RPM	45.27 RPM
SRP007412_cerebellum	0.00 RPM	24.43 RPM
SRP007412_heart	0.00 RPM	28.74 RPM
SRP007412_kidney	0.00 RPM	41.62 RPM
SRP007412_liver	0.00 RPM	24.43 RPM
SRP007412_testis	0.41 RPM	34.60 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_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1731 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2185
Macaca mulatta	retro_mmul_913

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731 , retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,