RetrogeneDB ID: retro_cjac_3300

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:47945014..47945514(-)
• Located in intron of: ENSCJAG00000006423

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX4I1
• Ensembl ID: ENSCJAG00000017319
• Aliases: None
• Description: cytochrome c oxidase subunit IV isoform 1 [Source:HGNC Symbol;Acc:2265]

Sequence

>retro_cjac_3300
ATGTTGGCTACCAGGGTATTTAGCCTAGTTGGCAAGCGAGCAATTTCCACCTCGGTGTGTGTACGAGCACACGGAAGTGT
TGTGAAGAGTGAAGACTATACGCTCCCAAGTTACGTGGATCGGCAAGAGACTATCCCTTGCCCGAAGTGGCCCATGTTAG
GCACCTGTCAGCCAGCCAGAAGGCCTTGAAGGAGGAGGAGGAGGCCTTCTGGAGCAGCCTCTCAATGGATGAGAAAGTCG
AGTTGTATCGTATTCAGTTCAAGGAGAGCTTTGCTGAGATGAACAGGGGCTCCAATGAGTGGAAGATGGTTGTGGGTGCT
GCCATGTTCTTCATCGGCTTTACAGCAATTCTTATCATCTTGGAGAAGTGCTATGTGTACGGCCCCCTCCCGCATACCTT
TGACAATGAGTGAGTGGCCATGCAGACCCAGAGGATACTGGACCTGAAGGTGAACCCCGTCGATGGCCTCGCTTCCAAGT
GGGACTATGACAAGAAGGAG

Alignment

ORF - retro_cjac_3300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.69 %
• Parental protein coverage: 98.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLATRVFSLVGKRAISTSVCVRAHGSVVKSEDYALPSYMDRRD-YPLP-DVAHVRHLSASQKALKEKEKA
          MLATRVFSLVGKRAISTSVCVRAHGSVVKSEDY.LPSY.DR....P.P..VAHVRHLSASQKALKE.E.A
Retrocopy MLATRVFSLVGKRAISTSVCVRAHGSVVKSEDYTLPSYVDRQETIPCP<EVAHVRHLSASQKALKEEEEA

Parental  SWSSLSVDEKVELYRIQFKESFAEMNRGSNEWKTVVGAAMFFIGFTAILIILEKRYVYGPLPHTFDKEWV
          .WSSLS.DEKVELYRIQFKESFAEMNRGSNEWK.VVGAAMFFIGFTAILIILEK.YVYGPLPHTFD.E.V
Retrocopy FWSSLSMDEKVELYRIQFKESFAEMNRGSNEWKMVVGAAMFFIGFTAILIILEKCYVYGPLPHTFDNE*V

Parental  AMQTKRMLDLKVNPVDGLASKWDYDKKE
          AMQT.R.LDLKVNPVDGLASKWDYDKKE
Retrocopy AMQTQRILDLKVNPVDGLASKWDYDKKE

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	0.42 RPM	47.33 RPM
SRP051959_heart	0.56 RPM	93.79 RPM
SRP051959_kidney	1.75 RPM	77.01 RPM
SRP051959_liver	0.63 RPM	57.49 RPM
SRP051959_lung	0.37 RPM	34.83 RPM
SRP051959_lymph_node	0.07 RPM	35.04 RPM
SRP051959_skeletal_muscle	0.35 RPM	112.71 RPM
SRP051959_spleen	0.11 RPM	34.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3300 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005479	1 retrocopy	retro_acar_90,
Ailuropoda melanoleuca	ENSAMEG00000018274	1 retrocopy	retro_amel_470,
Bos taurus	ENSBTAG00000016079	2 retrocopies	retro_btau_1406, retro_btau_483,
Canis familiaris	ENSCAFG00000019921	2 retrocopies	retro_cfam_1259, retro_cfam_1906,
Callithrix jacchus	ENSCJAG00000017319	4 retrocopies	retro_cjac_2267, retro_cjac_3264, retro_cjac_3300 , retro_cjac_802,
Dasypus novemcinctus	ENSDNOG00000017207	3 retrocopies	retro_dnov_2207, retro_dnov_2396, retro_dnov_737,
Equus caballus	ENSECAG00000011722	1 retrocopy	retro_ecab_418,
Felis catus	ENSFCAG00000007612	2 retrocopies	retro_fcat_1484, retro_fcat_853,
Homo sapiens	ENSG00000131143	1 retrocopy	retro_hsap_1428,
Gorilla gorilla	ENSGGOG00000010047	1 retrocopy	retro_ggor_1101,
Loxodonta africana	ENSLAFG00000014002	1 retrocopy	retro_lafr_528,
Macaca mulatta	ENSMMUG00000006763	4 retrocopies	retro_mmul_1129, retro_mmul_1285, retro_mmul_1724, retro_mmul_2260,
Mus musculus	ENSMUSG00000031818	2 retrocopies	retro_mmus_1305, retro_mmus_2958,
Nomascus leucogenys	ENSNLEG00000011409	1 retrocopy	retro_nleu_1843,
Oryctolagus cuniculus	ENSOCUG00000001735	5 retrocopies	retro_ocun_1238, retro_ocun_1333, retro_ocun_317, retro_ocun_469, retro_ocun_889,
Ochotona princeps	ENSOPRG00000002129	4 retrocopies	retro_opri_1205, retro_opri_267, retro_opri_821, retro_opri_857,
Pongo abelii	ENSPPYG00000007619	3 retrocopies	retro_pabe_1183, retro_pabe_1184, retro_pabe_996,
Pan troglodytes	ENSPTRG00000008434	1 retrocopy	retro_ptro_977,
Rattus norvegicus	ENSRNOG00000017817	1 retrocopy	retro_rnor_1157,
Tarsius syrichta	ENSTSYG00000009682	2 retrocopies	retro_tsyr_2073, retro_tsyr_591,