RetrogeneDB ID: retro_ptro_3055

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392651.1:127869..128533(-)
• Located in intron of: ENSPTRG00000008803

Retrocopy information

• Ensembl ID: ENSPTRG00000041192
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2S
• Ensembl ID: ENSPTRG00000011507
• Aliases: None
• Description: Ubiquitin-conjugating enzyme E2S [Source:UniProtKB/TrEMBL;Acc:K7BPT6]

Sequence

>retro_ptro_3055
AACTCCAACGTGGAGAACCTGCCCCCGCACATCATCCGCCTGGTGTACAAGGAGGTGACGACACTGACCGCAGACCCACC
CGATGGCATCAAGGTCTTTCCCAACGAGGAGGACCCTCACCGACCTCCAGGTCACCATCGAGGGCCCTGAGGGGACCCCA
TATGCTGGAGGTCTGTTCCGCATGAAACTCCTGCTGGGAAAGGACTTCCCTGCCTCCCCACCCAAGAGCTACTTCCTGAC
CAAGATCTTCCACCCGAACGTGGGCGCCAATGGCGAGATCTGCGTCAACGTGCTCAAGAGGGACTGGACAGCTGAGCTGG
GCATCTGACACGTACTGCTGACCATCAAGTGCCTGCTGACCCACCCTAACCCCGAGTCTGCACTCAACGAGGAGGCGGGC
CGCCTGCTCTTGGAGAACTACGAGGAGTATGCGGCTCGGGCCCGTCTGCTCACAGAGATCCACGGGGGCGCCGGCGGGCC
CAGCGGCAGGGCGGAAGCCGGTCGGGCCCTGGCCAGTGGCACTGCAGCTTCCTCCACCGACCCTGGGGCCCCAGGGGGCC
TGGGGGGGGCTGAGGGTCCCATGGCCAAGAAGCATGCTGGCGAGCGCGATAAGAAGCTGGCGGCCAACAAAAAGACGGAC
AAGAAGCGGGCGCTGCGGCGGCTG

Alignment

ORF - retro_ptro_3055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEED-LTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF
          NSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEED.LTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF
Retrocopy NSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEED>LTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF

Parental  PASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLEN
          PASPPK.YFLTKIFHPNVGANGEICVNVLKRDWTAELGI.HVLLTIKCLL.HPNPESALNEEAGRLLLEN
Retrocopy PASPPKSYFLTKIFHPNVGANGEICVNVLKRDWTAELGI*HVLLTIKCLLTHPNPESALNEEAGRLLLEN

Parental  YEEYAARARLLTEIHGGAGGPSGRAEAGRALASGTAASSTDPGAPGGPGGAEGPMAKKHAGERDKKLAAK
          YEEYAARARLLTEIHGGAGGPSGRAEAGRALASGTAASSTDP.........EGPMAKKHAGERDKKLAA.
Retrocopy YEEYAARARLLTEIHGGAGGPSGRAEAGRALASGTAASSTDPXXXXXXXXXEGPMAKKHAGERDKKLAAN

Parental  KKTDKKRALRRL
          KKTDKKRALRRL
Retrocopy KKTDKKRALRRL

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
SRP007412_brain_prefrontal_cortex	1.25 RPM	20.43 RPM
SRP007412_cerebellum	0.22 RPM	8.39 RPM
SRP007412_heart	0.03 RPM	2.94 RPM
SRP007412_kidney	0.10 RPM	4.29 RPM
SRP007412_liver	0.13 RPM	3.80 RPM
SRP007412_testis	2.00 RPM	41.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3055 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000874	3 retrocopies	retro_cjac_1995, retro_cjac_3689, retro_cjac_406,
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,