RetrogeneDB ID: retro_ptro_484

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:43475726..43476648(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSPTRG00000000583
• Aliases: None
• Description: adenylyl cyclase-associated protein 1 [Source:RefSeq peptide;Acc:NP_001233522]

Sequence

>retro_ptro_484
ATGACTGAAATGCAAAATCTGGTAAAAAATTGGACAGGGCAGTGGGCCGCCTGGAGGCAGTATCCCATACCTCTGACATG
CACCGTGGATATGGAGATAGTCCTTCAAAAGCAGGAGCAGCTCCATATGCTCAGGCATTTGACTCGCTGCTTGCCTGCCC
TGTGGCAGAGTACTTGAAGATCAGTAAAGAGATTGGGGAAGATGTGCAGAAAGATGTGGAGATGGTACACACAGTTTTGA
AGTTGGAGTGAGCTCTCTTGGTTACAGCTTCTCAGTGTCAATAGCCGGCAGGTAATAAGCTTTCCGATTTGTTGGCACCT
ATCTCAGAGCAGATCCAAGAAGTGATAACCTTTTGGGAGAAGAACCGAGGCAGCAAGTTGTTTAATCAGCTGTCAGCTGT
CAGTGAAAGTATCCAGGCCCTAGGCTGGGTGGCTATGGCTCCCAATCCTGGCCCTTATGTGAAAGAAATGAATCATGCTG
CTGTGTTTTATACAAACTGAGTCCTTAAAGAGTACAAAGATGTGGATAAGAAGCATGTAGACTGAGTCAAAGCTTATTTA
AGTATATGCACAGAGCTGCAGGCTTACATTAAGGAGTTCCATACCACCGGACTGCCTGGAGCAAAACGGGGCCTGTGACA
AAAGAACTGAGTGGACTGCCATCTGGACCCTCTGCTGGATCAGCTACTCCTCCCCCACCACCAGGCCCCCCTCCTCCACT
AGTCTTTGTCAGTTCAGGCTCAGATGAGTCCGCTTCCCTCTCAGCACTGTTTGCGCAGATTAATCAGGGGGAGAGCATCA
CACATGCCCTGAAACGTGTATCTGATGACATGAAGACTCACAAGAACCCTACCCTGAAGGCTCAGAGTGGTCCAGTACGC
GGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCAGC

Alignment

ORF - retro_ptro_484 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..MQNLV...L.RAVGRLEAVSHTSDMHRGY.DSPSKAGAAPY.QAFDSLLA.PVAEYLKISKEIG.DV
Retrocopy MTEMQNLVK<KLDRAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYAQAFDSLLACPVAEYLKISKEIGEDV

Parental  QKHAEMVHTGLKLERALLVTASQCQQPAENKLSDLLAPISEQIKEVITFREKNRGSKLFNHLSAVSESIQ
          QK..EMVHT.LKLE.ALLVTASQCQ.PA.NKLSDLLAPISEQI.EVITF.EKNRGSKLFN.LSAVSESIQ
Retrocopy QKDVEMVHTVLKLE*ALLVTASQCQ*PAGNKLSDLLAPISEQIQEVITFWEKNRGSKLFNQLSAVSESIQ

Parental  ALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGL-AWS
          ALGWVAMAP.PGPYVKEMN.AA.FYTN.VLKEYKDVDKKHVD.VKAYLSI.TELQAYIKEFHTTGL.AWS
Retrocopy ALGWVAMAPNPGPYVKEMNHAAVFYTN*VLKEYKDVDKKHVD*VKAYLSICTELQAYIKEFHTTGL<AWS

Parental  KTGPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVSTSSGSDESASRSALFAQINQGESITHALKHVSDDM
          KTGPV.KELSGLPSGPSAGS..PPPPPGPPPP.V..SSGSDESAS.SALFAQINQGESITHALK.VSDDM
Retrocopy KTGPVTKELSGLPSGPSAGSATPPPPPGPPPPLVFVSSGSDESASLSALFAQINQGESITHALKRVSDDM

Parental  KTHKNPALKAQSGPVRSGPKPFSAPKPQTS
          KTHKNP.LKAQSGPVR.GPKPFSAPKPQTS
Retrocopy KTHKNPTLKAQSGPVRGGPKPFSAPKPQTS

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	0.02 RPM	104.37 RPM
SRP007412_cerebellum	0.07 RPM	100.95 RPM
SRP007412_heart	0.00 RPM	53.31 RPM
SRP007412_kidney	0.00 RPM	145.38 RPM
SRP007412_liver	0.00 RPM	137.16 RPM
SRP007412_testis	0.63 RPM	193.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_484 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_484 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_664
Gorilla gorilla	retro_ggor_575
Pongo abelii	retro_pabe_584

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 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 ,
Pan troglodytes	ENSPTRG00000017750	1 retrocopy	retro_ptro_987,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,