RetrogeneDB ID: retro_cjac_406

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:70681519..70682187(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2S
• Ensembl ID: ENSCJAG00000000874
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2S [Source:HGNC Symbol;Acc:17895]

Sequence

>retro_cjac_406
ATGAACTCCAACGTGGAGAACCTGCCCCCGCACATCATCTGCCTGGTGTACAAGGAGGTGACGACACTGACCACAGACCC
ACCCGATGGCATCAAGGTCTTTCCCAACGAGGAGGACCTCACTGACCTCCAGGTCACCATCGAGGGCCCTGAGGGGACCC
CATATGCTGGAGGTCTGTTCCGCATGAAACTCCTGCTGGGGAAGGACTTCCCTGCCTCCCCACCCAAGGGCTACTTCCTA
ACCAAGATCTTCCACCCTAACGTGGGTGCCAATGGCGAGATCTGCGTCAACGTGCTCTAGAGGGACTGGACAGCTGAGCT
GGGCATCCGGCAGTGCTGCTGACCATCAGGTGCCTGTGATCCACCCTAACCCCGAGCCTGCACTCAACGAGGAGGCTGGC
CGCCTTCTCCTCGAGAACTATGAGGAGTATGTGGCTCGGCCCGTCTGCTCACAGAGATCCACGGGGATGCTGGTGGGCCC
AGTGGCAGGGCCGAAGCTGGTCGTGCCCTGGCCAGTGGCAGTGCAGCCTCCTCCACCGATCCTGGGGCCCCAGGGGCCCG
GGGTGGGGGGAGGCTGAGGGTCCCATGGCCAAGAAGCATGCTGGCGAGTGAGACAAGAAGCTGGCGGCCAAGAAAAAGAC
GGACAAGAAGCGGGCACTGCAGCGTCTG

Alignment

ORF - retro_cjac_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNSNVENLPPHIIRLVYKEVTTLTTDPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGVFRMKLLLGKDF
          MNSNVENLPPHII.LVYKEVTTLTTDPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGG.FRMKLLLGKDF
Retrocopy MNSNVENLPPHIICLVYKEVTTLTTDPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF

Parental  PASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRH-VLLTIKCL-LIHPNPESALNEEAGRLLL
          PASPPKGYFLTKIFHPNVGANGEICVNVL.RDWTAELGIR..VLLTI.CL..IHPNPE.ALNEEAGRLLL
Retrocopy PASPPKGYFLTKIFHPNVGANGEICVNVL*RDWTAELGIRQ<VLLTIRCL<VIHPNPEPALNEEAGRLLL

Parental  ENYEEYAAR-ARLLTEIHGGAGGPSGRAEAGRALASGTAASSTDPGAPG-GPGGAE--GPMAKKHAGERD
          ENYEEY.AR.ARLLTEIHG.AGGPSGRAEAGRALASG.AASSTDPGAPG.GPG..E..GPMAKKHAGE.D
Retrocopy ENYEEYVAR<ARLLTEIHGDAGGPSGRAEAGRALASGSAASSTDPGAPG<GPGWGEAEGPMAKKHAGE*D

Parental  KKLAAKKKTDKKRALRRL
          KKLAAKKKTDKKRAL.RL
Retrocopy KKLAAKKKTDKKRALQRL

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	5.15 RPM
SRP051959_heart	0.00 RPM	4.07 RPM
SRP051959_kidney	0.00 RPM	2.06 RPM
SRP051959_liver	0.00 RPM	1.06 RPM
SRP051959_lung	0.00 RPM	3.76 RPM
SRP051959_lymph_node	0.00 RPM	3.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.09 RPM
SRP051959_spleen	0.00 RPM	3.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_406 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000874	3 retrocopies	retro_cjac_1995, retro_cjac_3689, retro_cjac_406 ,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Homo sapiens	ENSG00000108106	1 retrocopy	retro_hsap_1808,
Mus musculus	ENSMUSG00000060860	2 retrocopies	retro_mmus_1675, retro_mmus_3278,
Pan troglodytes	ENSPTRG00000011507	2 retrocopies	retro_ptro_3055, retro_ptro_3059,
Rattus norvegicus	ENSRNOG00000016930	2 retrocopies	retro_rnor_1730, retro_rnor_912,