RetrogeneDB ID: retro_cjac_1995

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:25612836..25613482(+)
• 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_1995
ATGAACTCCAATGTGAAGAACCTGCCCCCACATATCATCCGCCTGGTGTACAAGGAGGTGACGACACTGACTGGAGACCC
ACCCAATGGCATCAAGGTCTTTCCCAACAAGGAGGACCTCACCAACCTCCAGGTCACCATCGAGGGCCCTGAGGGGACAC
CATATGCCAGAGGTCTGTTCTGCATGAAACTCCTGCTGGGGAAGGACTTCCTTGCCTCCCCACCCAAGGGCTACATCCTG
ACCAAGATCTTCCACCCGAATGTGGGCGCCAATGGTGAGATCTGGGCAACGTGCTCAAGAGGGACTGGAAAGCTGAGCTG
GGCATCTGACACATGCTGCTGACCATTACGTGCCTACTGATCCACCCTAACCCTGAGTCTGCCACGCAACGAGGAGGCGG
GCCGCCTTCTCCTTGAGAACTATGAGGAGTATGCGGCTCAGCTCCTCTGCTCACAGAGATCCACGGGGTGCTGGTGGGCC
CAGTGGCAGGACCGAAGTTGTTTGCGCTCTGGCTAGTGGCACTGCAGCCTCCTCCACCGATCCTGGGGCCCCAGGAGGCC
CAGGAGGGGCTGAGGGTCCCATGGCCAATAAGCATGCTGGCGAGCATGACAAGAAGCTGGCAGCCAAGAAAAAGACAGAC
AAGGAA

Alignment

ORF - retro_cjac_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 97.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNSNVENLPPHIIRLVYKEVTTLTTDPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGVFRMKLLLGKDF
          MNSNV.NLPPHIIRLVYKEVTTLT.DPP.GIKVFPN.EDLT.LQVTIEGPEGTPYA.G.F.MKLLLGKDF
Retrocopy MNSNVKNLPPHIIRLVYKEVTTLTGDPPNGIKVFPNKEDLTNLQVTIEGPEGTPYARGLFCMKLLLGKDF

Parental  PASPPKGYFLTKIFHPNVGANGEICV-NVLKRDWTAELGIRHVLLTIKCLLIHPNPESAL-NEEAGRLLL
          .ASPPKGY.LTKIFHPNVGANGEI...NVLKRDW.AELGI.H.LLTI.CLLIHPNPESA..NEEAGRLLL
Retrocopy LASPPKGYILTKIFHPNVGANGEIWA<NVLKRDWKAELGI*HMLLTITCLLIHPNPESAT>NEEAGRLLL

Parental  ENYEEYAAR-ARLLTEIHG-GAGGPSGRAEAGRALASGTAASSTDPGAPGGPGGAEGPMAKKHAGERDKK
          ENYEEYAA..A.LLTEIHG.GAGGPSGR.E...ALASGTAASSTDPGAPGGPGGAEGPMA.KHAGE.DKK
Retrocopy ENYEEYAAQ<APLLTEIHG<GAGGPSGRTEVVCALASGTAASSTDPGAPGGPGGAEGPMANKHAGEHDKK

Parental  LAAKKKTDKK
          LAAKKKTDK.
Retrocopy LAAKKKTDKE

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	0.04 RPM	5.15 RPM
SRP051959_heart	0.09 RPM	4.07 RPM
SRP051959_kidney	0.04 RPM	2.06 RPM
SRP051959_liver	0.02 RPM	1.06 RPM
SRP051959_lung	0.07 RPM	3.76 RPM
SRP051959_lymph_node	0.07 RPM	3.58 RPM
SRP051959_skeletal_muscle	0.04 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_1995 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1995 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,