RetrogeneDB ID: retro_pabe_2415

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3_random:3896435..3897734(-)
• 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_2415
CCATATGTGCAGGCATTTGACTCGCTGTTTGCTGGTGCTGTGGCAGAGTACTTGAAGATCAGTAAAGAGACTGAGGGAGA
CGTGCAGAAATATGCGGAGATGGTCCACACAGGTTTGAAGTTGGAGCGAGCTCTGTTGGTTACAGCTTCTCAGTGTCAAC
AGCCAGCAGATAATAAGCTTTCCAATTTGTTGGCACCCACCTCAGAGCAGATCAAAGAAGTGATAACCTTTCGGGAGAAG
AACCGAGGCAACAAGTTGTTTAATCACCTGTCAGCTGTCAGTGAAAGTATCCAGGCCCTGGGCTGGGTGGCTATGGCTCC
CAAGCCTGGCCCTTATGTGAAATAAATGAATGATGCTGCCATGTTTTATACAAACCAAGTCCTCAAAGAGTACAAAGATG
TGGATAAGAAGCATGTAGATGGGTCAAAGCTTATTTAAGTATATGGACAGAGCTGCAGGCTCACATTAAGGAGTTCCATA
CCACCGGACTGCCTGGAGCAAAACGGGGCTGTGGCAAAAGAACTGAGTGGACTCTGCCATCTGGACCCTCTGAGGGATCA
GGTCCTCCTCCCCCTCCACCAGGCCCCCTCCTCCCCTAGTGTCTACCAGTTCAGGCTCAGATGAGTCCACTTCCCGCTCA
GCACTGTTTGCGCAGATTAATCAGGGGGAGAGCATCACACATGCCCTGAATCATGTATCTGATGACATGAAGACTCACAA
GAACCCTGCCCTGAAGGCTCAGAGTGGTCCAGTACGCAGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCAGCC
CATCCTCCAAACCAGCCACAAAGAAGGAGCCAGCTGTACTTGAACTGGAGGGCAAGAAGTGGAGAGTGGAACATCAGGAA
AATGTTTCCAACCTGGTGATTGAGGACACAGAGCTGAAACAAATGGCTTACATATACAAGTGTGTCCACATGACATTGCA
AATCAAGGGCAAAATGAACGCCATTACAGTAGCTAACTGTAAGAAGCTTGGTCTGTATTCGATGACGTGGTGAGCATTGT
GGAGATAATCAGCAGTAAGGATGTCAAAGTTCAGGTAATGGGTAAAGTGCCAACCACATCCATCAACAAAACAGATGGCT
GCCATGCTTACCTGAGCAAGAATTCCCTGGATTGTGAAATAGTCAGTGCCAAATCTTCCGAGATGAACGCCCTCATTCCT
ACAGAAGGCGGTGACTTTAATGAATTCCCAGTTCCTGAGCAGTTCCAGACCCTAGGGCATGGGCAGAAGTTGGTCACCAG
AGTGACAGAAATTGCTGGA

Alignment

ORF - retro_pabe_2415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 91.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PYVQVFDSLLAGPVAEYLKISKEIGGDVQKHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQ
          PYVQ.FDSL.AG.VAEYLKISKE..GDVQK.AEMVHTGLKLERALLVTASQCQQPADNKLS.LLAP.SEQ
Retrocopy PYVQAFDSLFAGAVAEYLKISKETEGDVQKYAEMVHTGLKLERALLVTASQCQQPADNKLSNLLAPTSEQ

Parental  IKEVITFREKNRGSKLFNHLSAVSESIQALGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVD
          IKEVITFREKNRG.KLFNHLSAVSESIQALGWVAMAPKPGPYVK.MNDAAMFYTN.VLKEYKDVDKKHVD
Retrocopy IKEVITFREKNRGNKLFNHLSAVSESIQALGWVAMAPKPGPYVK*MNDAAMFYTNQVLKEYKDVDKKHVD

Parental  -WVKAYLSIWTELQAYIKEFHTTGLAWSKTGPVAKELSGLPSGPSAGSGPPPPPPGP-PPPPVSTSSGSD
          .WVKAYLSIWTELQA.IKEFHTTGL...K.G........LPSGPS.GSGPPPPPPGP.PPP.VSTSSGSD
Retrocopy <WVKAYLSIWTELQAHIKEFHTTGLPGAKRGCGKRTEWTLPSGPSEGSGPPPPPPGP<PPPLVSTSSGSD

Parental  ESASRSALFAQINQGESITHALKHVSDDMKTHKNPALKAQSGPLRSGPKPFSAPKPQTSQSPKPATKKEP
          ES.SRSALFAQINQGESITHAL.HVSDDMKTHKNPALKAQSGP.RSGPKPFSAPKPQTS.S.KPATKKEP
Retrocopy ESTSRSALFAQINQGESITHALNHVSDDMKTHKNPALKAQSGPVRSGPKPFSAPKPQTSPSSKPATKKEP

Parental  AVLELEGKKWRVENQENVSNLVIEDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGL-VFDDVVGI
          AVLELEGKKWRVE.QENVSNLVIEDTELKQ.AYIYKCV..TLQIKGK.N.ITV.NCKKLGL.VFDDVV.I
Retrocopy AVLELEGKKWRVEHQENVSNLVIEDTELKQMAYIYKCVHMTLQIKGKMNAITVANCKKLGL<VFDDVVSI

Parental  VEIINSRDVKVQVMGKVPTISINKTDGCHAYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFK
          VEII.S.DVKVQVMGKVPT.SINKTDGCHAYLSKNSLDCEIVSAKSSEMN.LIPTEGGDFNEFPVPEQF.
Retrocopy VEIISSKDVKVQVMGKVPTTSINKTDGCHAYLSKNSLDCEIVSAKSSEMNALIPTEGGDFNEFPVPEQFQ

Parental  TLWNGQKLVTTVTEIAG
          TL..GQKLVT.VTEIAG
Retrocopy TLGHGQKLVTRVTEIAG

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	0.00 RPM	22.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2415 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2415 has 0 orthologous retrocopies within eutheria group .

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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,