RetrogeneDB ID: retro_cjac_2259

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:111247964..111248817(-)
• Located in intron of: ENSCJAG00000005110

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSCJAG00000013548
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_cjac_2259
ATGGCCAACTTCAATGATTGTGTGTCAGATGAGAAGGTACCCATAGCTGTTAAGTTCGTCACTCATGCACCCCAGGGGAA
TTTAATGAACTATTTAATGATGTTTGGCTACTACTTAATAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATTTTC
CCAGTATAACATGGATCGGTTCATGTCTGTGAAGATAGAAGGATATGAAGATCAGGTTTTAATTACAGGGCATGGTGACC
TAGGTAACAGCAGATTTTTAGATCCAAGAAACAAAATTTCCTTTAAATTTGATCACCTAGGAAAGAAGCAAGTGACCCCC
ACCCAGAAGAAGCTGATGGAGGTCTTAAGTCTTGGAGAGAATCTTGTGACTGTGCTTTACCAGCCTATGTGAAAGACCAT
TATTCCAGCGGCTTCTGTACTGTTTATGCGAAAACTATCCATGGGCAACAGACTATTATTGCATGTATTGAAAGCCACCA
GTTACAGCCTAAAAACTTCTGGAATGGTAGTTGGAGATCAGAGCAGAAGTTCACCATCACACTACCTACAGCCCAGGTGG
TTGGAGTGCTTAAGACTCAGGTTCACTATTATGAAGATGGCAATGTTCAGTTGGCTAGTCATAAAGATGTACAGGATTGA
CTAACTGTTTTGAATGAAGCCCAAACTGCCAAGGAGTTTATTAATATCACAGAGAATGCAGAAAATGAGTATCAGACAGC
AATTAGTAAAAACTATCAAACAATGCCAGATACCACATTTAAGGCATTGCGCAGGCAGCTTCCATTTACCCACACCAAAA
TCAACTGGAACAAGATAGTCAGCTACAAGATTGGCAAAGAAATGCAGAATGCT

Alignment

ORF - retro_cjac_2259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADFDDRVSDEEKVRIAAKFITHAP-PGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEG
          MA.F.D.VSDE.KV.IA.KF.THAP.PGEFNE.FNDV.LLLNNDNLLREGAAHAF.QYNMD.F..VKIEG
Retrocopy MANFNDCVSDE-KVPIAVKFVTHAP<PGEFNELFNDVWLLLNNDNLLREGAAHAFSQYNMDRFMSVKIEG

Parental  YEDQVLITEHGDLGNSRFLDPRNKISFKFDHL-RKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSN
          YEDQVLIT.HGDLGNSRFLDPRNKISFKFDHL.RKEASDP.PEE.DGGLKSWRESCD.AL.AYVKDHYS.
Retrocopy YEDQVLITGHGDLGNSRFLDPRNKISFKFDHL<RKEASDPHPEEADGGLKSWRESCDCALPAYVKDHYSS

Parental  GFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVS
          GFCTVYAKTI.GQQTIIACIESHQ.QPKNFWNG.WRSE.KFTIT.PTAQVVGVLK.QVHYYEDGNVQL.S
Retrocopy GFCTVYAKTIHGQQTIIACIESHQLQPKNFWNGSWRSEQKFTITLPTAQVVGVLKTQVHYYEDGNVQLAS

Parental  HKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYK
          HKDVQD.LTV.NEAQTAKEFI.I.ENAENEYQTAIS.NYQTM.DTTFKALRRQLP.T.TKI.WNKI.SYK
Retrocopy HKDVQD*LTVLNEAQTAKEFINITENAENEYQTAISKNYQTMPDTTFKALRRQLPFTHTKINWNKIVSYK

Parental  IGKEMQNA
          IGKEMQNA
Retrocopy IGKEMQNA

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
SRP051959_colon	1.15 RPM	60.86 RPM
SRP051959_heart	0.61 RPM	25.77 RPM
SRP051959_kidney	0.78 RPM	43.09 RPM
SRP051959_liver	0.48 RPM	41.44 RPM
SRP051959_lung	1.06 RPM	66.75 RPM
SRP051959_lymph_node	1.14 RPM	114.84 RPM
SRP051959_skeletal_muscle	0.20 RPM	16.33 RPM
SRP051959_spleen	0.90 RPM	92.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2259 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2259 has 0 orthologous retrocopies within eutheria group .

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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,