RetrogeneDB ID: retro_ptro_1796

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:77827730..77829039(+)
• 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_1796
GCTCCATATGTGCAAGCATTTGACTCACTGCTTGCTGGTCCTGTGGCAGAGTATTTGAAGATCAGTAAAGAGACTGGGGG
AGATGTGCAGAAATATGCGGAGATGGTCCACACAGGTTTGACGTTGGAGCGAGCGCTGTTGGTTACAGCTTCTCAGTGTC
AACAGCCAGCAGATAATAAGCTTTCCAATTTCTTGGCACCCATCTCAGAGCAGATCAAAGAAGTGATAACCTTTCGGGAG
AAGAACCGAGGCAGCAAGTTGTTTAATCACCTGTCAGCTGTCAGCGAAAGTATCCAGGCCCTGGGCTGGGTGGCTATGGC
CCCCAAGCCTGGCCCTTATGTGAAAGAAATGAATGATGCTGCCATGTTTTATACAAACCGAGTCCTCAAAGAGTACAAAG
ATGTGGATAAGAAGCATGTAGACTGGGTCAAAGCTTATTTAAGTATATGGACAGAGCTGCAGGCTTACATTAAGGAGTTC
CATACCACTGGACTGCCTGGAGCAAAACGGGGCTGTGGCAAAAGAACTGAGTGGACTCTGCCATCTGGACCCTCTGCTGG
ATCAGGTCCTCCTCCCCGTTCACCAGGCAGGCCCCCCTCCTCCCCCAGTCTCTACCAGTTGAGGCTCAGATGAGTCCGCT
TCCCGCTCAGCCCTGTTTGCGCAGATTAATCAGGGGGAGAGCATCACACATGCCCTGAATCATGTATCTGATAACATGAA
GACTCACAAGAACCCTGCCCTGAAGGCTCAGAGTGGTCCAGTACGCAGTGGCCCCAAGCCATTCTCTGCACCTAAACCCC
AAACCAGCCCATCCCCCAAACCAGCCACAAAGAAGGAGCCAGCTGTACTTGAACTGGAGGGTAAGAAGTGGAGAGTGGAA
AATCAGGAAAATGTTTCCAACCTGGTGATTGAGGACGCAGAGCTGAAACAAATGGCTTACATATACAAGTGTGTCAACAT
GACATTGCAAATCAAGGGCAAAATGAACTCCATTACAGTAGATAACTGTAAGAAGCTTGGTCTGGTATTTGATGACATGG
TGGGCATTGTGGAGATAATCAACAGTAGGGATGTCAAAGTTCAGGTAATGGGTAAAGTGCCAACCATATCCATCAACAAA
ACAGATGGCTGCCATGCTTACCTGAGCAAGAATTCCCTGGATTGTGAGATAGTCAGTGCCAAATCTTCCTAGATGAACGC
CCTCATTCCTACAGAAGGCGGTGACTTTAATGAATTCCCAGTTCTTGAGCAGTTCAAGACCCTACAGCATGGGCAGAAGT
TGGTCACCACAGTGACAGAAATTGCTGGA

Alignment

ORF - retro_ptro_1796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 91.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APYVQAFDSLLAGPVAEYLKISKEIGGDVQKHAEMVHTGLKLERALLVTASQCQQPAENKLSDLLAPISE
          APYVQAFDSLLAGPVAEYLKISKE.GGDVQK.AEMVHTGL.LERALLVTASQCQQPA.NKLS..LAPISE
Retrocopy APYVQAFDSLLAGPVAEYLKISKETGGDVQKYAEMVHTGLTLERALLVTASQCQQPADNKLSNFLAPISE

Parental  QIKEVITFREKNRGSKLFNHLSAVSESIQALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHV
          QIKEVITFREKNRGSKLFNHLSAVSESIQALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHV
Retrocopy QIKEVITFREKNRGSKLFNHLSAVSESIQALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHV

Parental  DWVKAYLSIWTELQAYIKEFHTTGLAWSKTGPVAKELSGLPSGPSAGSGP-PPPP-PGPPPPPVSTSSGS
          DWVKAYLSIWTELQAYIKEFHTTGL...K.G........LPSGPSAGSGP.P..P..GPPPPPVSTS.GS
Retrocopy DWVKAYLSIWTELQAYIKEFHTTGLPGAKRGCGKRTEWTLPSGPSAGSGPPPRSP>AGPPPPPVSTS*GS

Parental  DESASRSALFAQINQGESITHALKHVSDDMKTHKNPALKAQSGPVRSGPKPFSAPKPQTSPSPKRATKKE
          DESASRSALFAQINQGESITHAL.HVSD.MKTHKNPALKAQSGPVRSGPKPFSAPKPQTSPSPK.ATKKE
Retrocopy DESASRSALFAQINQGESITHALNHVSDNMKTHKNPALKAQSGPVRSGPKPFSAPKPQTSPSPKPATKKE

Parental  PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGI
          PAVLELEGKKWRVENQENVSNLVIED.ELKQ.AYIYKCVN.TLQIKGK.NSITVDNCKKLGLVFDD.VGI
Retrocopy PAVLELEGKKWRVENQENVSNLVIEDAELKQMAYIYKCVNMTLQIKGKMNSITVDNCKKLGLVFDDMVGI

Parental  VEIINSKDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFK
          VEIINS.DVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSS.MN.LIPTEGGDFNEFPV.EQFK
Retrocopy VEIINSRDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSS*MNALIPTEGGDFNEFPVLEQFK

Parental  TLWNGQKLVTTVTEIAG
          TL..GQKLVTTVTEIAG
Retrocopy TLQHGQKLVTTVTEIAG

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	0.21 RPM	104.37 RPM
SRP007412_cerebellum	0.07 RPM	100.95 RPM
SRP007412_heart	0.09 RPM	53.31 RPM
SRP007412_kidney	0.10 RPM	145.38 RPM
SRP007412_liver	0.00 RPM	137.16 RPM
SRP007412_testis	0.21 RPM	193.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1796 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1796 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2666
Pongo abelii	retro_pabe_2212

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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,