RetrogeneDB ID: retro_cjac_2981

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:61083479..61083869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016002
• Aliases: None
• Description: None

Sequence

>retro_cjac_2981
ATGGAGACTTTGTATTGTGTCCCGTTCTTAGTGCTCGAATGTCCCAACCTGAAGCTAAAGAAACCGCCCTGGCTGCACAT
GGCGTTGGCCTTGACTGTGTATGCTTTGGTGGTGGTGTCTTGCTTTCTCATCACCAGAGGAATAATTTGTGACATTATTG
CTGAACCTCCAAATTTTGGCCCTATGACTGATGAACATGTGTATCAGAGGCCAGTAGCTTTCTTGGCCTACAGAGTAAAT
GGACAATATATTATGGAAGGACTTGCATCCAGCTTCCTGTTTACAATGGGAGGTTTAGGTTTCATAATCCTGGACCGATT
TAATGTATCAAATATCCCAAAACACAATAGATTTTTTCTTCTATTCATTGGATTCATCTGTGTCCTGTTG

Alignment

ORF - retro_cjac_2981 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 87.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQR
          METLY.VPFLVLECPNLKLKKPPWLHM..A.TVYALVVVS.FLIT.GII.D.I.EPP..G.MTDEH..QR
Retrocopy METLYCVPFLVLECPNLKLKKPPWLHMALALTVYALVVVSCFLITRGIICDIIAEPPNFGPMTDEHVYQR

Parental  PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLL
          PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDR.N..NIPK.NRF.LLFIGF.CVLL
Retrocopy PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRFNVSNIPKHNRFFLLFIGFICVLL

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	0.00 RPM	19.28 RPM
SRP051959_heart	0.00 RPM	5.93 RPM
SRP051959_kidney	0.00 RPM	14.73 RPM
SRP051959_liver	0.00 RPM	28.46 RPM
SRP051959_lung	0.02 RPM	10.12 RPM
SRP051959_lymph_node	0.02 RPM	13.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.11 RPM
SRP051959_spleen	0.00 RPM	15.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2981 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2981 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_370

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Bos taurus	ENSBTAG00000011611	1 retrocopy	retro_btau_753,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981 , retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Dasypus novemcinctus	ENSDNOG00000011172	2 retrocopies	retro_dnov_12, retro_dnov_1973,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Homo sapiens	ENSG00000198856	7 retrocopies	retro_hsap_1746, retro_hsap_2013, retro_hsap_2972, retro_hsap_3598, retro_hsap_3686, retro_hsap_376, retro_hsap_4246,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222, retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Myotis lucifugus	ENSMLUG00000000478	2 retrocopies	retro_mluc_1366, retro_mluc_1511,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297, retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,
Tursiops truncatus	ENSTTRG00000003446	1 retrocopy	retro_ttru_582,