RetrogeneDB ID: retro_cjac_925

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:75213507..75213875(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSCJAG00000007875
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_cjac_925
GAGGAATTGACAGATTTGCAGAGGGAGCCTTCTGCTTAGCGTTCACTGGGGCTGTGGGTGATGACTCAATGCTCCAGCTG
TCCATCATCTTGGGTCTGAATGAGAGTCCTTACCAAAGAGGCATTTTCTTTCTGACCGTGCACTTCCCTAGTGCTTACTC
TTGTAAGACACCAAAGGTTGCTTTCACAACCAAAATGTTTCTCTCCAATATACAGCAATGGTAGCCTCTCCTTCTGTACC
CTGTGTCTCAGTGGTCTCCAGCACTAACAGTGTCCAAGTTCTCTTACCCATCTGTTGCTTGCTCTGCAACCCCTACCCTG
CCGACCCTTTGGTGTGTAGAGACAGCCCACACCTACAAGGCTGACAGA

Alignment

ORF - retro_cjac_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.57 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EELTDLQRDPPAQCS-AGPVGDDLFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTKI-YH
          EELTDLQR.P.A..S..G.VGDD.......I.G.N.SPYQ.G.FFLT.HFP..Y..K.PKVAFTTK....
Retrocopy EELTDLQREPSA*RS<TGAVGDDSMLQLSIILGLNESPYQRGIFFLTVHFPSAYSCKTPKVAFTTKM>FS

Parental  PNINSNGSICLDILR-SQWSPALTVSK-VLLSICSLLCDPNPDDPLV-PEVAHTYKADR
          P.I.SNGS.....L..SQWSPALTVSK.VLL.IC.LLC.P.P.DPLV..E.AHTYKADR
Retrocopy P-IYSNGSLSFCTLC<SQWSPALTVSK<VLLPICCLLCNPYPADPLV>VETAHTYKADR

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	2.13 RPM
SRP051959_heart	0.00 RPM	9.98 RPM
SRP051959_kidney	0.00 RPM	9.34 RPM
SRP051959_liver	0.00 RPM	6.19 RPM
SRP051959_lung	0.00 RPM	5.45 RPM
SRP051959_lymph_node	0.00 RPM	3.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.16 RPM
SRP051959_spleen	0.00 RPM	4.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_925 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_925 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1067

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925 ,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Callithrix jacchus	ENSCJAG00000015818	9 retrocopies	retro_cjac_1813, retro_cjac_1815, retro_cjac_1998, retro_cjac_2073, retro_cjac_2511, retro_cjac_2576, retro_cjac_2856, retro_cjac_3174, retro_cjac_3296,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,