RetrogeneDB ID: retro_ptro_1710

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:163740398..163741259(-)
• Located in intron of: ENSPTRG00000012563

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSPTRG00000001110
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_ptro_1710
ATGGCCAACTTCAATGATTGTGTGTTGGATAAGGAGAAGGTATGCATAGCTGCTAAATTCATCACTCATGCACCCACAGG
AGAATTTAATGAAGTATTCAGTGATATTCGGCTACTATGTAATAATGACAGTCTCCTCAGGGAAAGGGCAGCACGTGCAT
TTGCCCATTATAACATGGATCAGTTCACACCCGTGAAGATGGAAGGATGTGAAGATCAGGTCATAATTACAGAGCATGGG
GGACCTGGGTAATAGCAGAGTTTTAGATCCAAGAAACAAAATTTCCTTTACATTTGATCACGTATAGAAAAAAGCAAGTG
ACCCCCAGCCAGAACAAGTAGATGGAGGTCTGAAGTCTTGGAGAGAATCCTGTGACAGTGCTTTAAGAGCCTATGTGAAA
GACCATTATTCCAACGGATTCTGTACTGTTTATGCTAAAAACTATCGATGGGCAACAGACTATTATTGCATGTATTGAAA
GCCATGAGTGTCAGCCTAAAAACTTCTGGAATGGTCGTTGGAGATCAGAGTGGAAGTTTACCATCACACCACCTACAGCC
CAGGTGGTTGGAGTGCTTAAGATTCAGGTTCACTATTACGAAGATGGCAGTGTTCAGTTGGTTAGTCATAAAGATGTACA
GGATTCGCTAACTGTTTCGAATGACGCACAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAATATC
AGACAGCAATTAGTGAAAACTGTCAAACAATGTCAGATACCACATTCAAGGTCTTGCGCCGGCAGCTTCCGGTTACCCGC
ACCAAAATTGACTGGAACAAGATTACTCAGCTACAACATTAGCAAAGAAATGCAGAATGCC

Alignment

ORF - retro_ptro_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADFDDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGY
          MA.F.D.V.D.EKV.IAAKFITHAP.GEFNEVF.D.RLL.NND.LLRE.AA.AFA.YNMDQFTPVK.EG.
Retrocopy MANFNDCVLDKEKVCIAAKFITHAPTGEFNEVFSDIRLLCNNDSLLRERAARAFAHYNMDQFTPVKMEGC

Parental  EDQVLITEHG-DLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSWRESCDSALRAYVKDHYSNG
          EDQV.ITEHG.DLGNSR.LDPRNKISF.FDH..K.ASDPQPE..DGGLKSWRESCDSALRAYVKDHYSNG
Retrocopy EDQVIITEHG>DLGNSRVLDPRNKISFTFDHV*KKASDPQPEQVDGGLKSWRESCDSALRAYVKDHYSNG

Parental  FCTVYAR-ITDGQ--IIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVS
          FCTVYA....DGQ..IIACIESH..QPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDG.VQLVS
Retrocopy FCTVYAK>TIDGQQTIIACIESHECQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGSVQLVS

Parental  HKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKI-LSY
          HKDVQDSLTVSN.AQTAKEFIKIIENAENEYQTAISEN.QTMSDTTFK.LRRQLPVTRTKIDWNKI.LSY
Retrocopy HKDVQDSLTVSNDAQTAKEFIKIIENAENEYQTAISENCQTMSDTTFKVLRRQLPVTRTKIDWNKI>LSY

Parental  KIGKEMQNA
          .I.KEMQNA
Retrocopy NISKEMQNA

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	0.79 RPM	10.64 RPM
SRP007412_cerebellum	0.82 RPM	14.66 RPM
SRP007412_heart	0.85 RPM	15.94 RPM
SRP007412_kidney	1.28 RPM	19.93 RPM
SRP007412_liver	1.18 RPM	20.43 RPM
SRP007412_testis	3.37 RPM	77.14 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1710 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1710 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2338
Gorilla gorilla	retro_ggor_1774
Pongo abelii	retro_pabe_2116
Macaca mulatta	retro_mmul_942

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 41 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,
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,