RetrogeneDB ID: retro_pabe_2212

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:42971403..42972705(+)
• 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_2212
GCTCCATATGTGCAGGCATTTGACTCGCTGTTTGCTGGTCCTGTGGCAGAGTACTTGAAGATCAGTAAAGAGACTGAGGG
AGACGTGCAGAAATATGCGGAGATGGTCCACACAGGTTTGAAGTTGGAGCGAGCTCTGTTGGTTACAGCTTCTCAGTGTC
AACAGCCAGCAGATAATAAGCTTTCCAATTTGTTGGCACCCACCTCAGAGCAGATCAAAGAAGTGATAACCTTTCGGGAG
AAGAACCGAGGCAACAAGTTGTTTAATCACCTGTCAGCTGTCAGTGAAAGTATCCAGGCCCTGGGCTGGGTGGCTATGGC
TCCCAAGCCTGGCCCTTATGTGAAATAAATGAATGATGCTGCCATGTTTTATACAAACTGAGTCCTCAAAGAGTACAAAG
ATGTGGATAAGAAGCATGTAGATGGGTCAAAGCTTATTTAAGTATATGGACAGAGCTGCAGGCTCACATTAAGGAGTTCC
ATACCACCGGACTGCCTGGAGCAAAATGGGGCTGTGGCAAAAGAACTGAGTGGACTCTGCCATCTGGACCCTCTGAGGGA
TCAGGTCCTCCTCCCCCTCCACCAGGCCCCCTCCTCCCCTAGTGTCTACCAGTTCAGGCTCAGATGAGTCCACTTCCCGC
TCAGCACTGTTTGCGCAGATTAATCAGGGGGAGAGCATCACACATGCCCTGAATCATGTATCTGATGACATGAAGACTCA
CAAGAACCCTGCCCTGAAGGCTCAGAGTGGTCCAGTACGCAGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCA
GCCCATCCTCCAAACCAGCCACAAAGAAGGAGCCAGCTGTACTTGAACTGGAGGGCAAGAAGTGGAGAGTGGAAAATCAG
GAAAATGTTTCCAACCTGGTGATTGAGGACACAGAGCTGAAACAAATGGCTTACATATACAAGTGTGTCCACACGACATT
GCAAATCAAGGGCAAAATGAACGCCATTACAGTAGCTAACTGTAAGAAGCTTGGTCTGTATTTGATGACGCGGTGAGCAT
TGTGGAGATAATCAGCAGTAAGGATGTCAAAGTTCAGGTAATGGGTAAAGTGCCAACCACATCCATCAACAAAACAGATG
GCTGCCATGCTTACCTGAGCAAGAATTCCCTGGATTGTGAAATAGTCAGTGCCAAATCTTCCAAGATGAACGCCCTCATT
CCTACAGAAGGCGGTGACTTTAATGAATTCCCAGTTCCTGAGCAGTTCCAGACCCTAGGGCATGGGCAGAAGTTGGTCAC
CAGAGTGACAGAAATTGCTGGA

Alignment

ORF - retro_pabe_2212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 91.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APYVQVFDSLLAGPVAEYLKISKEIGGDVQKHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISE
          APYVQ.FDSL.AGPVAEYLKISKE..GDVQK.AEMVHTGLKLERALLVTASQCQQPADNKLS.LLAP.SE
Retrocopy APYVQAFDSLFAGPVAEYLKISKETEGDVQKYAEMVHTGLKLERALLVTASQCQQPADNKLSNLLAPTSE

Parental  QIKEVITFREKNRGSKLFNHLSAVSESIQALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHV
          QIKEVITFREKNRG.KLFNHLSAVSESIQALGWVAMAPKPGPYVK.MNDAAMFYTN.VLKEYKDVDKKHV
Retrocopy QIKEVITFREKNRGNKLFNHLSAVSESIQALGWVAMAPKPGPYVK*MNDAAMFYTN*VLKEYKDVDKKHV

Parental  D-WVKAYLSIWTELQAYIKEFHTTGLAWSKTGPVAKELSGLPSGPSAGSGPPPPPPGP-PPPPVSTSSGS
          D.WVKAYLSIWTELQA.IKEFHTTGL...K.G........LPSGPS.GSGPPPPPPGP.PPP.VSTSSGS
Retrocopy D<WVKAYLSIWTELQAHIKEFHTTGLPGAKWGCGKRTEWTLPSGPSEGSGPPPPPPGP<PPPLVSTSSGS

Parental  DESASRSALFAQINQGESITHALKHVSDDMKTHKNPALKAQSGPLRSGPKPFSAPKPQTSQSPKPATKKE
          DES.SRSALFAQINQGESITHAL.HVSDDMKTHKNPALKAQSGP.RSGPKPFSAPKPQTS.S.KPATKKE
Retrocopy DESTSRSALFAQINQGESITHALNHVSDDMKTHKNPALKAQSGPVRSGPKPFSAPKPQTSPSSKPATKKE

Parental  PAVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGL-VFDDVVG
          PAVLELEGKKWRVENQENVSNLVIEDTELKQ.AYIYKCV.TTLQIKGK.N.ITV.NCKKLGL.VFDD.V.
Retrocopy PAVLELEGKKWRVENQENVSNLVIEDTELKQMAYIYKCVHTTLQIKGKMNAITVANCKKLGL<VFDDAVS

Parental  IVEIINSRDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQF
          IVEII.S.DVKVQVMGKVPT.SINKTDGCHAYLSKNSLDCEIVSAKSS.MN.LIPTEGGDFNEFPVPEQF
Retrocopy IVEIISSKDVKVQVMGKVPTTSINKTDGCHAYLSKNSLDCEIVSAKSSKMNALIPTEGGDFNEFPVPEQF

Parental  KTLWNGQKLVTTVTEIAG
          .TL..GQKLVT.VTEIAG
Retrocopy QTLGHGQKLVTRVTEIAG

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	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	0.03 RPM	22.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2212 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2212 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2212 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2666
Pan troglodytes	retro_ptro_1796

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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,