RetrogeneDB ID: retro_pabe_2266

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:163722940..163723888(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000014257
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: B3GAT3
• Ensembl ID: ENSPPYG00000025907
• Aliases: None
• Description: beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I) [Source:HGNC Symbol;Acc:923]

Sequence

>retro_pabe_2266
GATCGCCGGCCTCCTCTACGTGCTGGCCAGCCATGTGACTGCCTTCCTCCCCTGCGGGCAGCAGCCGAGCAGCTACGGCA
GAAGGATCTGAGGATTTCCCAACTGCAAGCGGAACTACGACGGCCACCCCCTGCCCCTGCCCAGCCCCCTGAACCCGAGG
CCCTGCCTACTATCTATGTTGTTACCCCCACCTATGCCAGGCTGGTACAGAAGGCAGAGCTGGTACAGCTGTCCCAGACA
CTGAGCCTGGTGCCCCGGCTGCATTGACTGCTGTTGGAGGATGCTGAGGGTCCCACCCCGCTGGTCTCAGGGCTGCTGGC
TGCCTCTGGCCTCCTCTTCACACACCTGGTGGTCCTCACGCCCAAAGCCCAGCGGCTTCGGGAGGGCGAGCCTGGCTGGG
TTCATCCCCGTGGTGTCGAGCAACGGAACAAGGCCCTGGACTGGCTCTGGGGCAGAGGGAGTGCTGTGGGTGGGGAGAAG
GACCCATCACCACCAGGGACCCAAGGAGTCGTGTACTTTGCTGACAATGACAACACCTACAGCCGGGAGCTGTTTGAGGA
GATGTGCTGGACCCGTGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGCGGCATGCGATTCGAGGGCCCTCAGGTACAGG
ACGGCCAGGTAGTGGGCTTCGACACAGCATGGGAGCCCAAGAGGCCCTTCCCTGTGGATATGGCCGGATTTGCTGTGGCC
CTGCCCTTGCTGTTAGCTAAGCCCAATGCCCAGTTTGATTCCACTGCTCCCCGGAGCCACCTGGAGAGCAGTCTTCTAAG
CCACCTTGTGGATCCCAAGGACCTGGAGCCACGGGCTGCCAACTGCACTCGGGTACTGTTGTGGCATACATGGACAGAGA
AGCCCAAGATGAAGCAGGAGGAGCAGCTGCAGCGGCAGGGCCGGGGCTCAGACCCAGCAATTGAGGTG

Alignment

ORF - retro_pabe_2266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.35 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSATALSSGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQ
          D....L..GQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQ
Retrocopy DRRPPLRAGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQ

Parental  KAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVE
          KAELV.LSQTLSLVPRLH.LL.EDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVE
Retrocopy KAELVQLSQTLSLVPRLH*LLLEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVE

Parental  QRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGP
          QRNKALDWL.GRG.AVGGEKDP.PPGTQGVVYFAD.DNTYSRELFEEM.WTRGVSVWPVGLVGG.RFEGP
Retrocopy QRNKALDWLWGRGSAVGGEKDPSPPGTQGVVYFADNDNTYSRELFEEMCWTRGVSVWPVGLVGGMRFEGP

Parental  QVQDGRVVGFHTAWEPNRPFPVDMAGFAVALPLLLAKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAA
          QVQDG.VVGF.TAWEP.RPFPVDMAGFAVALPLLLAKPNAQFDSTAPR.HLESSLLSHLVDPKDLEPRAA
Retrocopy QVQDGQVVGFDTAWEPKRPFPVDMAGFAVALPLLLAKPNAQFDSTAPRSHLESSLLSHLVDPKDLEPRAA

Parental  NCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV
          NCTRVL.WHT.TEKPKMKQEEQLQRQGRGSDPAIEV
Retrocopy NCTRVLLWHTWTEKPKMKQEEQLQRQGRGSDPAIEV

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	0.50 RPM	2.88 RPM
SRP007412_cerebellum	0.00 RPM	3.40 RPM
SRP007412_heart	0.03 RPM	0.33 RPM
SRP007412_kidney	0.27 RPM	1.59 RPM
SRP007412_liver	0.06 RPM	0.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2266 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2266 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2724
Pan troglodytes	retro_ptro_1841
Gorilla gorilla	retro_ggor_1896

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000149541	1 retrocopy	retro_hsap_2724,
Gorilla gorilla	ENSGGOG00000013604	1 retrocopy	retro_ggor_1896,
Nomascus leucogenys	ENSNLEG00000003956	1 retrocopy	retro_nleu_589,
Pongo abelii	ENSPPYG00000025907	1 retrocopy	retro_pabe_2266 ,
Pan troglodytes	ENSPTRG00000039665	1 retrocopy	retro_ptro_1841,