RetrogeneDB ID: retro_cjac_1203

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:44612876..44613460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003319
• Aliases: None
• Description: None

Sequence

>retro_cjac_1203
TTCATTACTGTCCCCTGAAACCCAAAGTGCCTCAAAGCAGGAAGGTGTGCCAACTATGTAGTGACTGGAGCCTGGTCAGC
TAAAGCTGCAGAAACTTCCAAGAAGTTTGAGATTGTGATTATCAGCTACCCTAAATGTGGAAGTTATATGAAAATACCAG
ATTCAAGCATCTGGAACCTCACCCTTACAGCTTCTATGTGTAATACTGCACAAATGACTGGCTCAGAGTGGCATTTGACT
TTATATCTGATCTAAGGAAGCACTACTAGTTTGCCACTTATCCTCAAACTTTCTGTTGAAGGCAGTGGATGCCTCCGGGT
TTGGTGTGACTTTTGCTGGTACCCAGAAGCACACTGGTTGTTCTGAGATGACAGTAGTGATTATCTGCAATGATTGCTGG
GGTCACCCTCAGAGAGTGGCCCTCCCTCCTGGAATACAAACTGCATGTTGGAAACAACTTCTTGTACAACATGCAACAGT
ATTTCAGCAACTATGTCATGGGCTTGTACCTGGTGTAGATTAAGAATGATGGCACTGAAGTAGTGATGGAGAAGCTTAGC
TCCATCAAATCTAAAATAATATTT

Alignment

ORF - retro_cjac_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.7 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FSAVPLNLIGLKAGRCADYVVTGSWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNL-NPDASYVYY
          F..VP.N...LKAGRCA.YVVTG.WSAKAAE..KKF....I..PK.GSY.KIPD.S.WNL..P...YV.Y
Retrocopy FITVP*NPKCLKAGRCANYVVTGAWSAKAAETSKKFEIVIISYPKCGSYMKIPDSSIWNL<HPYSFYV*Y

Parental  CANETVHGVEFDFIPDV-KGVVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDD-LLG-
          C.N.....V.FDFI.D..K...LVC..SSNFL.K.VD.S.FGV.FAG.QK..G....TVVI...D.LLG.
Retrocopy CTNDWLR-VAFDFISDL<KEALLVCHLSSNFLLKAVDASGFGVTFAGTQKHTGCSEMTVVIICND<LLG<

Parental  FALRECPSVLEYKVQAGNNSLYNTPPCFSIYVMGLVLEWIKNNGGAVAMEKLSSIKSQMIY
          ..LRE.PS.LEYK...GNN.LYN....FS.YVMGL.L..IKN.G..V.MEKLSSIKS..I.
Retrocopy VTLREWPSLLEYKLHVGNNFLYNMQQYFSNYVMGLYLV*IKNDGTEVVMEKLSSIKSKIIF

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	0.04 RPM	3.15 RPM
SRP051959_heart	0.05 RPM	0.44 RPM
SRP051959_kidney	0.02 RPM	0.91 RPM
SRP051959_liver	0.00 RPM	0.78 RPM
SRP051959_lung	0.05 RPM	0.75 RPM
SRP051959_lymph_node	0.02 RPM	3.04 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.24 RPM
SRP051959_spleen	0.00 RPM	1.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1203 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1203 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2267
Pan troglodytes	retro_ptro_1606
Pongo abelii	retro_pabe_1950

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203 ,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,