RetrogeneDB ID: retro_pabe_2299

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:34629227..34630610(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WWP1
• Ensembl ID: ENSPPYG00000018724
• Aliases: None
• Description: WW domain containing E3 ubiquitin protein ligase 1 [Source:HGNC Symbol;Acc:17004]

Sequence

>retro_pabe_2299
TGGGAAAAAAGAGTGGATTCAACAGACAGGGTTTACTTTGTGAATCATAATACAAAAACAACCCAGTGGGAAGATCTAAG
AACTCAAGGCTTACAGAATGAAGAACCTCTGCCAGAAGGCTGGGAAATTAGATATACTCGTGAAGGTGTAAGGTACTTTG
TTAATCATAACGCAAGAACAACAACATTCAAAGATCCTCGCAATGGGAAGTCATCTGTAACTAAAGGTGGTCCACAAATT
GATTATGAACACAGCTTTAGGCGGAAACTTGCTCACTTCCATTATTTGTGCCAGTCTAATGCACTACCCAGTCACGTAGA
GATCAATGTGTCCCGGCAGACATTGTTTGAAGATTCCTTCCAACAGATTATGGCATTAAAACCTTATGACTTGAGGAGGT
GCTTATATGTAATATTTAGAGGAGAAGAAGGACTTGATTATGGTGGCCTAGCAAGAGAATGGCTTTTCTTGCTTTCACAT
GAAGTTTTGAACACAATGTATTGCTTATTTGAGTATGCAGGGAAGAACAACTATTGCCTGCAGATAAATCCAGCATCAAC
CATTAATCCAGACCATCTTTCATACTTCTGTTTCATTGGTCGTTTTATTGCCACGGCACTATTTCATGGAAAGTTTATCG
ATACTGATTTCTCTTTACCATTCTACAAGCGTATGTTAAGTGAAAAACTTACTATTAAGGATTTGGAATCTATTGATACT
GAATTTTATAACTCCCTTATCTGGATAAGAGATAACAACATTGAAGAATGTGGCTTAGAACCGTACTTTTCTGTTGACAT
GGAGAGTTGGGGAAAAGTTACCTTACATGACCCGAAGTTGGGAGTTTCCAATATTCTGGTGACTGAGGAGAACAAAGATG
AATATATTGGTTTAATGACAGAATGGCATTTTTCTCGAGGAGTACAAGAACAGACCAAAACTTTCCTTGATGGTTTTAAT
GGAGTTGTTCCTCGTCAGCGGCTACAGTACTTCGATGAAAAAGATTTAGAGGTTATGTTGTGAGGCACGCAGGAGGCTGA
CTTGGCAGATTGGCAGAGAAATACTCTTTATCAACATTATACAAGAAACAGCAAGCAAATCATTCGGTTTCGGCAGTTTG
TGAAAGAGACAGACAATGAAGTAAGAATGCTACTATCGCAGTTCGTCACTGGAACCTGCCGTTTATCTCTAGGAGGATTT
GCTGAGCTCATGGGAAGTAATGGGACTCAAAAGTTTTGCATTGAAAAAGTTGGCAAAGACACTTGGTTACCAAGAAGCCA
TACGTGTTTTAATCTCTTGGATCTACCACCATATAAGATTTACAAACAACTAAAGGAAAAACTTCTTTTTGCAATAGAAG
AGACAGAGGGATTTGGACAAGAA

Alignment

ORF - retro_pabe_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSKRVDSTDRVYFVNHNTKTTQWEDPRTQGLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTTFKDPRNGK
          ..KRVDSTDRVYFVNHNTKTTQWED.RTQGLQNEEPLPEGWEIRYTREGVRYFV.HN.RTTTFKDPRNGK
Retrocopy WEKRVDSTDRVYFVNHNTKTTQWEDLRTQGLQNEEPLPEGWEIRYTREGVRYFVNHNARTTTFKDPRNGK

Parental  SSVTKGGPQIAYERSFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFR
          SSVTKGGPQI.YE.SFR.KLAHF.YLCQSNALPSHV.INVSRQTLFEDSFQQIMALKPYDLRR.LYVIFR
Retrocopy SSVTKGGPQIDYEHSFRRKLAHFHYLCQSNALPSHVEINVSRQTLFEDSFQQIMALKPYDLRRCLYVIFR

Parental  GEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFHG
          GEEGLDYGGLAREW.FLLSHEVLN.MYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIA.ALFHG
Retrocopy GEEGLDYGGLAREWLFLLSHEVLNTMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIATALFHG

Parental  KFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKL
          KFIDT.FSLPFYKRMLS.KLTIKDLESIDTEFYNSLIWIRDNNIEECGLE.YFSVDME..GKVT.HD.KL
Retrocopy KFIDTDFSLPFYKRMLSEKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEPYFSVDMESWGKVTLHDPKL

Parental  GGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLAD
          G.SNILVTEENKDEYIGLMTEW.FSRGVQEQTK.FLDGFN.VVP.Q.LQYFDEK.LEVML.G.QE.DLAD
Retrocopy GVSNILVTEENKDEYIGLMTEWHFSRGVQEQTKTFLDGFNGVVPRQRLQYFDEKDLEVML*GTQEADLAD

Parental  WQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKD
          WQRNT.Y.HYTRNSKQII.F.QFVKETDNEVRM.L.QFVTGTCRL.LGGFAELMGSNG.QKFCIEKVGKD
Retrocopy WQRNTLYQHYTRNSKQIIRFRQFVKETDNEVRMLLSQFVTGTCRLSLGGFAELMGSNGTQKFCIEKVGKD

Parental  TWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE
          TWLPRSHTCFN.LDLPPYK.Y.QLKEKLLFAIEETEGFGQE
Retrocopy TWLPRSHTCFNLLDLPPYKIYKQLKEKLLFAIEETEGFGQE

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	0.28 RPM	16.81 RPM
SRP007412_cerebellum	0.97 RPM	21.65 RPM
SRP007412_heart	0.72 RPM	38.02 RPM
SRP007412_kidney	0.66 RPM	32.45 RPM
SRP007412_liver	1.50 RPM	66.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2299 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2299 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2680
Pan troglodytes	retro_ptro_1807
Macaca mulatta	retro_mmul_1418

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000123124	1 retrocopy	retro_hsap_2680,
Macaca mulatta	ENSMMUG00000006305	1 retrocopy	retro_mmul_1418,
Mustela putorius furo	ENSMPUG00000010807	1 retrocopy	retro_mputfur_963,
Mus musculus	ENSMUSG00000041058	1 retrocopy	retro_mmus_2017,
Nomascus leucogenys	ENSNLEG00000001517	1 retrocopy	retro_nleu_1183,
Pongo abelii	ENSPPYG00000018724	1 retrocopy	retro_pabe_2299 ,
Pan troglodytes	ENSPTRG00000020395	1 retrocopy	retro_ptro_1807,