RetrogeneDB ID: retro_cjac_3174

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:1051342..1051800(+)
• Located in intron of: ENSCJAG00000012237

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSCJAG00000015818
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_cjac_3174
GCCAGCAGGAGGCTGACGAAGCACATTGAATAAACCCACAAATGTGGAATGAAAACCTTCCATAACATCCAGGTTGATGA
AACTAATGTATTGACTTGGCAAGGGCTTACTGATCCTGACAACCCTCCGTATGATAGGGGAGCCTCAGAATAGAAATCAA
CTTCCCAGCAGAGTACCCATTCAAACCACCGAAGATCTCATTTAAAACAAAGATCTGTCACCCAAAGGTCGATGCTGAAA
AGGGGCAGGTCTGTCTGTCAGTAATTAGTGCCGAAAACTGGAAGCTAGCAACCAAAGCTGAACAAGTAATGCAATCCCTC
ATGGCAGTGGTGAACGACCCCCAGCCTGAGCACCTGCTGCAGGCTGACCTAGCTGAAGAATAGTTTAAGGACAGTAAAAC
ATTCCTCAAGAATACTGAGGTGTTTGTAGAGAAATATGGGGAAAACCGACCTGTGGAC

Alignment

ORF - retro_cjac_3174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGA-FRIEINFPAEYPFKPPKITFK
          ASRRL.K..E...KCGMK.F.NIQVDE.N.LTWQGL..PDNPPYD.GA..RIEINFPAEYPFKPPKI.FK
Retrocopy ASRRLTKHIE*THKCGMKTFHNIQVDETNVLTWQGLTDPDNPPYDRGA<LRIEINFPAEYPFKPPKISFK

Parental  TKIYHPNID-EKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNA
          TKI.HP..D.EKGQVCL.VISAENWK.ATK..QV.QSL.A.VNDPQPEH.L.ADLAEE..KD.K.F.KN.
Retrocopy TKICHPKVDAEKGQVCLSVISAENWKLATKAEQVMQSLMAVVNDPQPEHLLQADLAEE*FKDSKTFLKNT

Parental  EEFTKKYGEKRPVD
          E.F..KYGE.RPVD
Retrocopy EVFVEKYGENRPVD

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	1.60 RPM	20.01 RPM
SRP051959_heart	5.42 RPM	16.33 RPM
SRP051959_kidney	0.60 RPM	20.39 RPM
SRP051959_liver	0.95 RPM	13.60 RPM
SRP051959_lung	0.34 RPM	20.53 RPM
SRP051959_lymph_node	0.25 RPM	22.17 RPM
SRP051959_skeletal_muscle	0.22 RPM	14.52 RPM
SRP051959_spleen	0.55 RPM	22.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3174 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3174 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
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	ENSDORG00000011406	1 retrocopy	retro_dord_357,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Gorilla gorilla	ENSGGOG00000028073	3 retrocopies	retro_ggor_1425, retro_ggor_861, retro_ggor_924,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,