RetrogeneDB ID: retro_pabe_2116

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:49206684..49207203(-)
• Located in intron of: ENSPPYG00000012872

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSPPYG00000001021
• Aliases: None
• Description: F-actin-capping protein subunit alpha-1 [Source:RefSeq peptide;Acc:NP_001127090]

Sequence

>retro_pabe_2116
GATGGAGGTCGGATGTCTTGGAGAGAATCCTGTGACAGTGCTTTAAGAGCCAATGTGAAAGACCGTTATTCCAACGGCTT
CTGTACTGTTTATGCTAAAACTATCGATGGGCAACAGACTATTATTGCATGTATTGAAAGCCATGAGTGTCAGCCTAAAA
ACTTCTGGAATGGTCTTTGGAGATCAGAGTGGAAGTTTACCATCACACCACCTACAGCCCAGGTGGTTGGAGTCTTAAGA
TTCAGGCTCACTATTATGAAGATGGCAGTGTTCAGTTGGTTAGTCGTAAGGATGTACAGGATTCACTAACTGTTTCGAAT
GACGCACAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAATATCAGACAGCAATTAGTGAAAACTG
TCAAACAATGTCAGATACCACATTCAAGGTCTTGAGCCGGCAGCTTCCGGTTACCCGCACCAAAATTGACTGGAACAAGA
TTACTCAGCTACAACGTTGGCAAAGAAATGCAGAATGCC

Alignment

ORF - retro_pabe_2116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGGLKSWRESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITP
          DGG..SWRESCDSALRA.VKD.YSNGFCTVYAKTIDGQQTIIACIESH..QPKNFWNG.WRSEWKFTITP
Retrocopy DGGRMSWRESCDSALRANVKDRYSNGFCTVYAKTIDGQQTIIACIESHECQPKNFWNGLWRSEWKFTITP

Parental  PTAQVVGV-LKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSD
          PTAQVVGV.LKIQ.HYYEDG.VQLVS.KDVQDSLTVSN.AQTAKEFIKIIENAENEYQTAISEN.QTMSD
Retrocopy PTAQVVGV<LKIQAHYYEDGSVQLVSRKDVQDSLTVSNDAQTAKEFIKIIENAENEYQTAISENCQTMSD

Parental  TTFKALRRQLPVTRTKIDWNKI-LSYKIGKEMQNA
          TTFK.L.RQLPVTRTKIDWNKI.LSY..GKEMQNA
Retrocopy TTFKVLSRQLPVTRTKIDWNKI>LSYNVGKEMQNA

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	22.34 RPM
SRP007412_cerebellum	0.00 RPM	34.90 RPM
SRP007412_heart	0.09 RPM	21.28 RPM
SRP007412_kidney	0.00 RPM	33.18 RPM
SRP007412_liver	0.03 RPM	54.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2116 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2116 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2338
Pan troglodytes	retro_ptro_1710
Gorilla gorilla	retro_ggor_1774
Macaca mulatta	retro_mmul_942

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116 , retro_pabe_3789,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,