RetrogeneDB ID: retro_ggor_1774

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:47025228..47026089(-)
• Located in intron of: ENSGGOG00000016720

Retrocopy information

• Ensembl ID: ENSGGOG00000024112
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSGGOG00000012158
• Aliases: None
• Description: F-actin-capping protein subunit alpha-2 [Source:UniProtKB/Swiss-Prot;Acc:Q2IBE7]

Sequence

>retro_ggor_1774
ATGGACAACTTCAATGATTGTGTGTTGGATAAGGAGAAGGTATGCATAGCTGCCAAATTCATCACTCATGCACCCGCAGG
AGAATTTAATGAAGTATTCAGTGATATTCGGCTACTATGTAATAATGACAGTCTCCTCAGGGAAAGGGCAGCATGTGCAT
TTGCCCATTATAACATGGATCAGTTCACACCCGTGAAGATGGAAGGATATGAAGATCAGGTCATAATTACAGAGCGTGGG
GGACCTGGGTAATAGCAGAGTTTTAGATCCAAGAAACAAAATTTCCTTTACATTTGATCACTTATAGAAAAAAGCAAGTG
ACCCCCAGCCAGAACAAGTAGATGGAGGTCTGAAGTCTTGGAGAGAATCCTGTGACAGTGCTTTAGGAGCCTATTTGAAA
GACCATTATTCCAACGGCTTCTGTACTGTTTATGCTAAAAACTATCGATGGGCAACAGACTATTATTGCATGTATTGAAA
GCCATGAGTGTCAGCCTAAAAACTTCTGGAATGGTCGTTGGAGATCAGAGTGGAAGTTTACCATCACACCACCTACAGCC
CAGGTGGTTGGAGTGCTTAAGATTCAGGTTCACTATTACGAAGATGGCAGTGTTCAGTTGGTTAGTCATAAAGATGTACA
GGATTCGCTAACTGTTTTGAATGACGCACAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAATATC
AGACAGCAGTTAGTAAAAACTGTCAAACAATGTCAGATACCACATTCAAGGTCTTGCGCCGGCAGCTTCCGGTTACCCGC
ACCAAAATTGACTGGAACAAGATTACTCAGCCACAACATTAGCAAAGAAATGCAGAATGCC

Alignment

ORF - retro_ggor_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADLEEQLSDEEKVRIAAKFIIHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNLDQFTPVKIEGY
          M........D.EKV.IAAKFI.HAP.GEFNEVF.D.RLL.NND.LLRE.AA.AFA.YN.DQFTPVK.EGY
Retrocopy MDNFNDCVLDKEKVCIAAKFITHAPAGEFNEVFSDIRLLCNNDSLLRERAACAFAHYNMDQFTPVKMEGY

Parental  EDQVLITEHG-DLGNGKFLDPKNRICFKFDHLRKEATDPRPCEVENAVESWRTSVETALRAYVKEHYPNG
          EDQV.ITE.G.DLGN...LDP.N.I.F.FDHL.K.A.DP.P..V.....SWR.S...AL.AY.K.HY.NG
Retrocopy EDQVIITERG>DLGNSRVLDPRNKISFTFDHL*KKASDPQPEQVDGGLKSWRESCDSALGAYLKDHYSNG

Parental  VCTVYGKK-IDGQQTIIACIESHQFQAKNFWNGRWRSEWKFTITPSTTQVVGILKIQVHYYEDGNVQLVS
          .CTVY.K..IDGQQTIIACIESH..Q.KNFWNGRWRSEWKFTITP.T.QVVG.LKIQVHYYEDG.VQLVS
Retrocopy FCTVYAKN>IDGQQTIIACIESHECQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGSVQLVS

Parental  HKDIQDSLTVSNEVQTAKEFIKIVEAAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKI-LSY
          HKD.QDSLTV.N..QTAKEFIKI.E.AENEYQTA.S.N.QTMSDTTFK.LRRQLPVTRTKIDWNKI.LS.
Retrocopy HKDVQDSLTVLNDAQTAKEFIKIIENAENEYQTAVSKNCQTMSDTTFKVLRRQLPVTRTKIDWNKI>LSH

Parental  KIGKEMQNA
          .I.KEMQNA
Retrocopy NISKEMQNA

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	1.97 RPM	47.19 RPM
SRP007412_cerebellum	2.17 RPM	28.33 RPM
SRP007412_heart	0.72 RPM	16.07 RPM
SRP007412_kidney	4.21 RPM	96.95 RPM
SRP007412_liver	2.77 RPM	41.33 RPM
SRP007412_testis	18.54 RPM	40.09 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_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1774 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2338
Pan troglodytes	retro_ptro_1710
Pongo abelii	retro_pabe_2116
Macaca mulatta	retro_mmul_942

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774 ,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,