RetrogeneDB ID: retro_cjac_657

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:4060845..4061267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D3
• Ensembl ID: ENSCJAG00000015492
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]

Sequence

>retro_cjac_657
ATGGCACTGAAACTTAGCTCTTTGGCCCGTGACCCTCCAGCACAATGCTCTGGCAGATCTGGTCAGGAATGATAAGTGTT
ATTGGCAAGTCACGATTATGGGACCTAATAGTCCATATCAAGTAGTGCTTACTTTTTGAAAATTTATTTTCTTATAAATC
AACCTAAGGTTGCATTGAAACCACTTAAGATTACATTTAAAATAATTTATCATCCACACCTTAACAGTAATGGCAATATT
TGCCTTGATATTTTAACATCAGTGTAGTCCGCGTAAACTATTTCCAAGGTTCTTTTATTCACTATTTTCCACTGCTGTGG
GATCCAAACCGGGAAGACCCTCTACTATCAGAGACTGCATGAAAATCAAAAACAAAGAAAAATCAATAAAATATCTTGGG
GTGGATTCAGAAGTATGACATG

Alignment

ORF - retro_cjac_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.01 %
• Parental protein coverage: 95.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSKELSDLARDPPAQCS-AGPVGDDMFHWQATIMGPNDSPYQ-GGVFFLTIHFPTDYP---FKPPKVAFT
          ....LS.LARDPPAQCS.A..V..D...WQ.TIMGPN.SPYQ.....FL.I.F....P....KP.K..F.
Retrocopy MALKLSSLARDPPAQCS>ADLVRNDKCYWQVTIMGPN-SPYQ<SSAYFLKIYFLINQPKVALKPLKITFK

Parental  TRIYHPNINSNGSICLDILRSQWSPALTISKVLL-SICSLLCDPNP-DDPLVPEIARIYKTDRDKYNRIS
          ..IYHP..NSNG.ICLDIL.S..S.A.TISKVLL.S..S......P..DPL..E.A...KT.....N...
Retrocopy I-IYHPHLNSNGNICLDILTSV*S-A*TISKVLL>SLFSTAVGSKP>EDPLLSETA*KSKTKKNQ*NILG

Parental  REWTQKYAM
          ..W.QKY.M
Retrocopy --WIQKYDM

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	93.96 RPM
SRP051959_heart	0.00 RPM	92.82 RPM
SRP051959_kidney	0.00 RPM	110.47 RPM
SRP051959_liver	0.00 RPM	103.21 RPM
SRP051959_lung	0.00 RPM	110.18 RPM
SRP051959_lymph_node	0.00 RPM	125.13 RPM
SRP051959_skeletal_muscle	0.00 RPM	114.85 RPM
SRP051959_spleen	0.00 RPM	106.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_657 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_657 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1156
Pongo abelii	retro_pabe_1257
Macaca mulatta	retro_mmul_2143

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
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,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Macropus eugenii	ENSMEUG00000004256	6 retrocopies	retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,