RetrogeneDB ID: retro_ptro_1171

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:24883227..24884259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040753
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR45L
• Ensembl ID: ENSPTRG00000009807
• Aliases: None
• Description: None

Sequence

>retro_ptro_1171
ATGAACCTCCTGCCGTGTAACCATCACCGCAACGGGCTGCTGTACGCTGGCTTCGACCAGGACCACAGATGCTTTGCGTG
TGGGATGGAAAATGGATTCCGAGTCTATAACACTGATCCACTAAATGAAAAAGAGAAACAAGAATTTCTAGAAGGAGGAG
TTGGCCATGTTGAAATGTTATTTCGCTGCAACTATTTAGCTTTAGTTGGTGGTGGAAAAAAGCCAAAATACCCTCCCAAC
AAAGTAATGATCTGGGATGACCTGAAGAAGAAGACTGTTATTGAAATAGAATTTTCTACAGAAGTCAAGGCAGTCAAACT
GCGGCGAGATAGAATTGTGGTGGTTTTGGACTCCGTAATTAAGGTGTTCACATTCACACACAATCCCCAATGGTTGCACA
TCTTGAAAACCTGCTATAACCCCAAAGGCCTCTGTGTCCTTTGTCCCAATAGTAACAACTCCCTCCTGGCCTTTCCGGGC
ACGCACACGGGCCACGTACAGCTTGTGGACCTGGCCAGCACAGAGAAGCCACCAGTGGACATTCCTGCACATGAGGGTGT
CCTGAGCTGCAGTGCACTCAAACTGCAGGGAACAAGAATTGCAACTGCATCCGAGAAAGGGACCCTTATAAGAATATTTG
ATACTTCCTCAGGGCATTTAATTCAGGAACTGCGAAGAGGATCTCAAGCAGCCAATATTTACTGCATTAACTTCAATCAG
GATGCGTCCCTCATCTGCGTATCCAGCGACCATGGCACAGTGCATATTTTTGCAGCTGAAGATCTAAAAAGGAATAAACA
GTCCAGTTTGGCCTCAGCCAGTTTCCTTCCAAAATACTTCAGTTACAAGTGGAGTTTCTCCAAGTTTCAGGTTCCCTCAG
GCTCTCCGTGCATTTGTGCCTTTGGAACACAGCCAAACGCCGTCATTGCAATTTGTGCAGACTGCAGCTACTACAAACTC
CTGTTCAACCCCAAGGGGGAGTGCATCCGAGATGTCTACGCGCAGTATCTAGAGATGACTGATGACAAGCTG

Alignment

ORF - retro_ptro_1171 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLLPCNPHGNGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVG
          MNLLPCN.H.NGLLYAGF.QDH.CFACGMENGFRVYNTDPL.EKEKQEFLEGGVGHVEMLFRCNYLALVG
Retrocopy MNLLPCNHHRNGLLYAGFDQDHRCFACGMENGFRVYNTDPLNEKEKQEFLEGGVGHVEMLFRCNYLALVG

Parental  GGKKPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCYN
          GGKKPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDS.IKVFTFTHNP..LH...TCYN
Retrocopy GGKKPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSVIKVFTFTHNPQWLHILKTCYN

Parental  PKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGTLI
          PKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSC.AL.LQGTRIATASEKGTLI
Retrocopy PKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCSALKLQGTRIATASEKGTLI

Parental  RIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLPKYF
          RIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAED.KRNKQSSLASASFLPKYF
Retrocopy RIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDLKRNKQSSLASASFLPKYF

Parental  SSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL
          S.KWSFSKFQVPSGSPCICAFGT.PNAVIAICAD.SYYK.LFNPKGECIRDVYAQ.LEMTDDKL
Retrocopy SYKWSFSKFQVPSGSPCICAFGTQPNAVIAICADCSYYKLLFNPKGECIRDVYAQYLEMTDDKL

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	0.34 RPM	75.52 RPM
SRP007412_cerebellum	0.25 RPM	130.92 RPM
SRP007412_heart	0.03 RPM	43.25 RPM
SRP007412_kidney	0.05 RPM	102.91 RPM
SRP007412_liver	0.07 RPM	85.14 RPM
SRP007412_testis	0.11 RPM	108.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1171 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1171 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1820
Gorilla gorilla	retro_ggor_2173
Pongo abelii	retro_pabe_150

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171 , retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,