RetrogeneDB ID: retro_cjac_1998

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:28502185..28502641(+)
• Located in intron of: ENSCJAG00000014460

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_1998
ATGGCGACCAGCAGGAGGCTGATGAAGCTTGAAGAAATCTGCAAATTGTGGAATGAAAAACTTCCGTAACATCCAGGTTG
ATGAAGCTAATTTACTGACTTGGCAAGGGCTTATTGTTCCTGACAACCCTCTGTATTATAAGGGACCTTCAGAATCGAAA
TCAGCTTTCCAGCCGAGTACCCATTCAAACCACAGAAGATCACATTTAAAACAAAGATCTATCACCTGAACATCGATGAA
AAGGGGCGGGTCTGTCTCCCAATAATTAGTGCTGAAAACTGGAAGCCAGCAACCAAAACCACCCAAGTAATCCAGTCCCT
CACAGCACTGGTGAATGACCCCCAGCCCAAGCCCCAGTTCGGGCTGACCTAGCTGAAGAATACTCTAAGGACTGTAAAAA
ATTCTGTAAGAATGCTGGAGTTTACAAAGAAATATGGGAAAAAGCAACCTGTGGAC

Alignment

ORF - retro_cjac_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELEEIRK-CGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKG-AFRIEINFPAEYPFKPPKI
          MA.SRRLMK.LEEI.K.CGMKNFRNIQVDEANLLTWQGLIVPDNP.Y.KG..FRIEI.FPAEYPFKP.KI
Retrocopy MATSRRLMK-LEEICK>CGMKNFRNIQVDEANLLTWQGLIVPDNPLYYKG<TFRIEISFPAEYPFKPQKI

Parental  TFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQP-EHPLRADLAEEYSKDRKKFC
          TFKTKIYH.NIDEKG.VCLP.ISAENWKPATKT.QVIQSL.ALVNDPQP...P.RADLAEEYSKD.KKFC
Retrocopy TFKTKIYHLNIDEKGRVCLPIISAENWKPATKTTQVIQSLTALVNDPQP<QAPVRADLAEEYSKDCKKFC

Parental  KNAEEFTKKYGEK-RPVD
          KNA....K...EK..PVD
Retrocopy KNAGVY-KEIWEK>QPVD

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	0.44 RPM	20.01 RPM
SRP051959_heart	0.23 RPM	16.33 RPM
SRP051959_kidney	0.27 RPM	20.39 RPM
SRP051959_liver	0.39 RPM	13.60 RPM
SRP051959_lung	0.63 RPM	20.53 RPM
SRP051959_lymph_node	0.87 RPM	22.17 RPM
SRP051959_skeletal_muscle	0.26 RPM	14.52 RPM
SRP051959_spleen	0.44 RPM	22.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1998 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1998 has 0 orthologous retrocopies within eutheria group .

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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,