RetrogeneDB ID: retro_pabe_584

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:42174360..42175282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSPPYG00000001496
• Aliases: None
• Description: adenylyl cyclase-associated protein 1 [Source:RefSeq peptide;Acc:NP_001126158]

Sequence

>retro_pabe_584
ATGACTGGCATGCAAAATCTGGTAGAAAAATTGGACAGGGCAGTGGGCCGCCTGGAGGCAGTATCCCATACCTCTGACGT
GCACCCTGGATATGGAGATAGTCCTTCAAAAGCAGGAGCAGCTCCATATGCGCAGGCATTTGACTCGCTGCTTGCCTGCC
CTGTGGCAGAGTACTTGAAGATCAGTAAAGAGATTGGGGGAGACGTGCAGAAAGGTGGAGATGGTCCACACATGTTTGAA
GTTGGAGTGAGCTCTCTTGATTACAGCTTCTCAGTGTCAACAGCCGGCAGGTAATAAGCTTTCCGATTTGTTGGCACCTA
TCTCAGAGCAGATCAAAGAAATGATAACCTTTTGGGAGAAGAACCGAGGCAGCAAGTTGTTTAATCAGCTGTCAGCTGTC
AGTGAAAGTATCCAGGCCCTAGGCTGGGTGGCTATGGCTCCCAATCCTGGCCATTATGTGAAAGAAATTAATCATGCTGC
TGTGTTTTATACAAACTGAGTCCTTAAAGAGTACAAAGATGTGGATAAGAAGTATGTAGACTGAGTCAAAGCTTATTTAA
GTATATGCACAGAGCTGCAGGCTTACATTAAGGAGTTCCATACCACCGGACTGCCTGGAGCAAAACGCGGCCTGTGACAA
AAGAACTGAGTGGACTGCCATCTGGACCCTCTGCTGGATCAGCTACTCCTCCCCCACCACCAGGCCCCCCTTCTCCACGA
GTCTCTGTCAGTTCAGGCTCAGATGAGTCCGCTTCCCTCTCAGCACTGTTTGCGCAGATTAATCAGGGGGAGAGCATCAC
ACATTCCCTGAAACGTGTTATCTGATGACATGAAGACTCACAAGAACCCTACCCTGAAGACTCAGAGTGGTCCAGTATGC
AGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCAGC

Alignment

ORF - retro_pabe_584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVERLERAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYVQVFDSLLAGPVAEYLKIS-KEIGGDV
          M..MQNLVE.L.RAVGRLEAVSHTSD.H.GYGDSPSKAGAAPY.Q.FDSLLA.PVAEYLKIS.K..G...
Retrocopy MTGMQNLVEKLDRAVGRLEAVSHTSDVHPGYGDSPSKAGAAPYAQAFDSLLACPVAEYLKIS>KRLGETC

Parental  QKHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQIKEVITFREKNRGSKLFNHLSAVSESIQ
          .K..EMVHT.LKLE.ALL.TASQCQQPA.NKLSDLLAPISEQIKE.ITF.EKNRGSKLFN.LSAVSESIQ
Retrocopy RK-VEMVHTCLKLE*ALLITASQCQQPAGNKLSDLLAPISEQIKEMITFWEKNRGSKLFNQLSAVSESIQ

Parental  ALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGL-AWS
          ALGWVAMAP.PG.YVKE.N.AA.FYTN.VLKEYKDVDKK.VD.VKAYLSI.TELQAYIKEFHTTGL.AWS
Retrocopy ALGWVAMAPNPGHYVKEINHAAVFYTN*VLKEYKDVDKKYVD*VKAYLSICTELQAYIKEFHTTGL<AWS

Parental  KTGPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVSTSSGSDESASRSALFAQINQGESITHALKHV-SDD
          KT.PV.KELSGLPSGPSAGS..PPPPPGPP.P.VS.SSGSDESAS.SALFAQINQGESITH.LK.V.SDD
Retrocopy KTRPVTKELSGLPSGPSAGSATPPPPPGPPSPRVSVSSGSDESASLSALFAQINQGESITHSLKRV>SDD

Parental  MKTHKNPALKAQSGPLRSGPKPFSAPKPQTS
          MKTHKNP.LK.QSGP..SGPKPFSAPKPQTS
Retrocopy MKTHKNPTLKTQSGPVCSGPKPFSAPKPQTS

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	0.17 RPM	47.33 RPM
SRP007412_cerebellum	0.00 RPM	13.86 RPM
SRP007412_heart	0.00 RPM	11.83 RPM
SRP007412_kidney	0.00 RPM	28.21 RPM
SRP007412_liver	0.00 RPM	22.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_584 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_584 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_664
Pan troglodytes	retro_ptro_484
Gorilla gorilla	retro_ggor_575

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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,