RetrogeneDB ID: retro_ggor_575

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:55394544..55395466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSGGOG00000027527
• Aliases: None
• Description: Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:G3SA10]

Sequence

>retro_ggor_575
ATGACTGACATGCAAAATCTGGTAAAAAATTGGACAGGGCAGTGGGCCGCCTGGAGGCAGTATCCCATACCTCTGACATG
CACCGTGGATATGGAGATAGTCCTTCAAAAGCAGGAGCAGCTCCATATGCGCAGGCATTTGACTCGCTGCTTGCCTGCCC
TGTGGCAGAGTACTTGAAGATCAGTAAAGAGATTGGGGAAGACGTGCAGAAAGATGTGGAGATGGTACACACAGGTTTGA
AGTTGGAGTGAGCTCTCTTGGTTACAGCTTCTCAGTGTCAATAGCCGGCAGGTAATAAGCTTTCCGATTTGTTGGCACCT
ATCTCAGAGCAGATCAAAGAAGTGATAACCTTTTGGGAGAAGAACCGAGGCGGCAAGTTGTTAAATCAGCTGTCAGCTGT
CAGTGAAAGTATCCAGGCCCTAGGCTGGGTGGCTATGGCTCCCAATCCTGGCCCTTATGTGAAAGAAATGAATCATGCTG
CTGTGTTTTATACAAACTGAGTCCTTAAAGAGTACAAAGATGTGGATAAGAAGCATGTAGACTGAGTCAAAGCTTATTTA
AGTATATGCACAGAGCTGCAGGCTTACATTAAGGAGTTCCATACCACCAGACTGCCTGGAGCAAAACGGGGCCTGTGACA
AAAGAACTGAGTGGACTGCCATCTGGACCCTCTGCTGGATCAACTACTCCTCCCCCACCACCAGGCCCCCCTCCTCCACT
AGTCTCTGTCAGTTCAGGCTCAGATGAGTCCACTTCCCTCTCAGCACTGTTTGCGCAGATTAATCAGGGGGAGAGCATCA
CACATGCCCTGAAACGTGTATCTGATGACATGAAGACTCACAAGAACCCTACCCTGAAGGCTCAGAGTGGTCCAGTACGC
AGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCAGC

Alignment

ORF - retro_ggor_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVE-RLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDV
          M.DMQNLV...L.RAVGRLEAVSHTSDMHRGY.DSPSKAGAAPY.QAFDSLLA.PVAEYLKISKEIG.DV
Retrocopy MTDMQNLVK<KLDRAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYAQAFDSLLACPVAEYLKISKEIGEDV

Parental  QKHAEMVHTGLKLERALLVTASQCQQPAENKLSDLLAPISEQIKEVITFREKNRGSKLFNHLSAVSESIQ
          QK..EMVHTGLKLE.ALLVTASQCQ.PA.NKLSDLLAPISEQIKEVITF.EKNRG.KL.N.LSAVSESIQ
Retrocopy QKDVEMVHTGLKLE*ALLVTASQCQ*PAGNKLSDLLAPISEQIKEVITFWEKNRGGKLLNQLSAVSESIQ

Parental  ALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGL-AWS
          ALGWVAMAP.PGPYVKEMN.AA.FYTN.VLKEYKDVDKKHVD.VKAYLSI.TELQAYIKEFHTT.L.AWS
Retrocopy ALGWVAMAPNPGPYVKEMNHAAVFYTN*VLKEYKDVDKKHVD*VKAYLSICTELQAYIKEFHTTRL<AWS

Parental  KTGPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVSTTSGSDESASRSALFAQINQGESITHALKHVSDDM
          KTGPV.KELSGLPSGPSAGS..PPPPPGPPPP.VS..SGSDES.S.SALFAQINQGESITHALK.VSDDM
Retrocopy KTGPVTKELSGLPSGPSAGSTTPPPPPGPPPPLVSVSSGSDESTSLSALFAQINQGESITHALKRVSDDM

Parental  KTHKNPALKAQSGPVRSGPKPFSAPKPQTS
          KTHKNP.LKAQSGPVRSGPKPFSAPKPQTS
Retrocopy KTHKNPTLKAQSGPVRSGPKPFSAPKPQTS

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	94.71 RPM
SRP007412_cerebellum	0.04 RPM	46.88 RPM
SRP007412_heart	0.00 RPM	21.11 RPM
SRP007412_kidney	0.00 RPM	137.71 RPM
SRP007412_liver	0.03 RPM	90.05 RPM
SRP007412_testis	0.83 RPM	144.94 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_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_575 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_664
Pan troglodytes	retro_ptro_484
Pongo abelii	retro_pabe_584

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575 ,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,