RetrogeneDB ID: retro_cjac_1971

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:155688574..155689222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021110
• Aliases: None
• Description: None

Sequence

>retro_cjac_1971
CCCTAGAAGTGGGGCTGTGACATGGCAAATAAAGAAAATGAACTGGTTTGTGCAGGTCACCTATCTGAAAAATTATGCCA
GACTGGTCAAATATATTTGTTTAACTCCAGTGATTCTGAGTTTTCACAGACAGAAAGCCCATCATTGTAATATAGTGGGT
ATTTTTTCTCAAATTTCTCAGGATCACAAAACAAATAGCTCAAGTTTTTTTGCTCAGCAGAAATTTGAAACTGAGAGTAG
CTTTAACTTTCTGGAGAAAGAAGTACAAGTGAAATTTGCAGCTTGTTTGGTAAGAATAGAAGATCTTGGCATTGAGGTAG
ATTGTCTTCCTGTGCTCACCAGTGGTTTACAGGGAGAAAAACAATACATCTTTCTTGAAGGCTGGGTAGGCTCACTGCCT
CTAGTAAAGTAGCTACGTAATAGCAAATTTGAAAAATACGTAACAGTTGGTTTAAACTGGCTTTAAGCAGTCATTAAAAG
GTGCTGATCAGAACAATTGTTCAAAACAGAAATTATAAATAATGAAAACATCCAGATTTAAAAACAACAGTTAAGTGAAT
TGTAGGAACAGGAAACCATCTGACTTTGGTTCTGGGATACACTGGTAATATAGCTAAGGAAGTGGATGTTTATTTATTAC
CAGTACAT

Alignment

ORF - retro_cjac_1971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.27 %
• Parental protein coverage: 83.01 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGSGGCDMANKENELACAGHLPEKLHHDSRTYLINSSDSGSSQTESPSSKYSGFF-SEVSQDHET-MAQV
          P...GCDMANKENEL.CAGHL.EKL......YL.NSSDS..SQTESPS..YSG.F.S..SQDH.T..AQV
Retrocopy P*KWGCDMANKENELVCAGHLSEKLCQTGQIYLFNSSDSEFSQTESPSL*YSGYF>SQISQDHKT>IAQV

Parental  -LFSRNLRLNVALTFWR-KRSISELVAYLLRIEDLGVVVDCLPVLTNSLQEEKQCISLGCCVDLLPLVKS
          .L.SRNL.L.VALTFWR.K.......A.L.RIEDLG..VDCLPVLT..LQ.EKQ.I.L...V..LPLVK.
Retrocopy FLLSRNLKLRVALTFWR<KEVQVKFAACLVRIEDLGIEVDCLPVLTSGLQGEKQYIFLEGWVGSLPLVK*

Parental  LLKSKFEEYVIVGLNWLQAVIKRWWSDLSSKTEIINDRNIQILKQQLSGLWEQE-NHLTLVPGYTGNIAK
          L..SKFE.YV.VGLNWL.AVIKR..S....KTEIIN..NIQI.KQQLS.L.EQE.NHLTLV.GYTGNIAK
Retrocopy LRNSKFEKYVTVGLNWL*AVIKRC*SEQLFKTEIINNENIQI*KQQLSEL*EQE<NHLTLVLGYTGNIAK

Parental  DVDAYLLQLH
          .VD.YLL..H
Retrocopy EVDVYLLPVH

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	13.93 RPM
SRP051959_heart	0.00 RPM	7.10 RPM
SRP051959_kidney	0.00 RPM	11.40 RPM
SRP051959_liver	0.00 RPM	5.98 RPM
SRP051959_lung	0.00 RPM	10.72 RPM
SRP051959_lymph_node	0.00 RPM	10.89 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.25 RPM
SRP051959_spleen	0.00 RPM	10.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1971 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1971 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3171
Gorilla gorilla	retro_ggor_1347
Pongo abelii	retro_pabe_2634
Macaca mulatta	retro_mmul_2005

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006413	2 retrocopies	retro_btau_1198, retro_btau_1776,
Callithrix jacchus	ENSCJAG00000021110	3 retrocopies	retro_cjac_1971 , retro_cjac_265, retro_cjac_2971,
Cavia porcellus	ENSCPOG00000011153	2 retrocopies	retro_cpor_1374, retro_cpor_1410,
Dasypus novemcinctus	ENSDNOG00000016279	5 retrocopies	retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii	ENSDORG00000013172	2 retrocopies	retro_dord_378, retro_dord_730,
Equus caballus	ENSECAG00000023450	1 retrocopy	retro_ecab_841,
Echinops telfairi	ENSETEG00000001640	7 retrocopies	retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens	ENSG00000134152	3 retrocopies	retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla	ENSGGOG00000014230	3 retrocopies	retro_ggor_1347, retro_ggor_2486, retro_ggor_415,
Macropus eugenii	ENSMEUG00000015610	4 retrocopies	retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus	ENSMLUG00000001532	2 retrocopies	retro_mluc_214, retro_mluc_633,
Macaca mulatta	ENSMMUG00000000013	1 retrocopy	retro_mmul_2005,
Mustela putorius furo	ENSMPUG00000008019	1 retrocopy	retro_mputfur_1258,
Nomascus leucogenys	ENSNLEG00000010772	2 retrocopies	retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus	ENSOCUG00000017654	5 retrocopies	retro_ocun_1065, retro_ocun_343, retro_ocun_614, retro_ocun_877, retro_ocun_975,
Otolemur garnettii	ENSOGAG00000015633	3 retrocopies	retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps	ENSOPRG00000010379	1 retrocopy	retro_opri_446,
Pongo abelii	ENSPPYG00000006309	2 retrocopies	retro_pabe_2634, retro_pabe_646,
Pan troglodytes	ENSPTRG00000006877	3 retrocopies	retro_ptro_2271, retro_ptro_2491, retro_ptro_323,
Sorex araneus	ENSSARG00000007891	1 retrocopy	retro_sara_345,
Ictidomys tridecemlineatus	ENSSTOG00000003813	1 retrocopy	retro_itri_1292,
Tupaia belangeri	ENSTBEG00000001614	7 retrocopies	retro_tbel_1267, retro_tbel_127, retro_tbel_1362, retro_tbel_2139, retro_tbel_3276, retro_tbel_4552, retro_tbel_984,
Tarsius syrichta	ENSTSYG00000011059	1 retrocopy	retro_tsyr_2135,
Vicugna pacos	ENSVPAG00000007170	1 retrocopy	retro_vpac_632,