RetrogeneDB ID: retro_ptro_1262

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:32063521..32064410(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ptro_1262
ATGATCCTCCTACCCTGTAACTCCCACAGTAACTAGCTGCTCTACACCGGCTTCAGCCAGGACCACGGATGCCTTGCTTG
TTGGATGGAAAACGGATTCTGAGTCTATAACACCAATCCATTAAAATAAAAAGAGAAACAAAAATTTCTAGGAGGAAGAG
TTGGTCATTATGAAATGTTATTTTGCTGCAACTATTTAGCTTTAGTTGTTGGTGGAAAAAAGCCAAAATACCTTCCCAAC
AAAGTGATGATCTGAGATGATGGAAAAAGAAGACTGTTAATGAAATAGAATTTGCTACAGAAGTCAAGGCAGTCAAATTG
CAGCGAGATAGAATTGTGGTTGTTTTGGACTCCATGATTAAGGTGTTTGCACTCACACAGAACCCCCATCAGTTGTACAT
CTTTGAAACCTCCTAAAACCCTAAAGGCCTCTGTCCTCTGTCCCAATAGCAACAACTCTCTTCTGGCCTTGCCGGGCACG
CACACGGGCCATGTTCAGCTCGTGGACTGGGCCAGCACAGAGAAGCCACCTGTGGACATTCCCGCCCTGAGGGCATCCTG
AGCTGCATCATACTCAACCTGCAGGGAACAAGAATTGCAACCACACTCGCAAAAGGGACCCTTTTAAGAATATTTGATAC
CTCATCAGGACATTTAATCCAGGAACTATGAAGAGGATCTCAAGCAGCTAATGTTTTCTGCATTAACTTCAGTCAAGATG
AGTCCTTCATCTGCATATCCAGTGACCACAGCACAGTGCACATTTTTGCAGCTGAAGACCCAGGAAGGAATAAACAGTCC
AATTTGGTGTCAGCTAGTTTCCTTCCAAAATCCTTTAGTTGCAAAGGGGTTTCTCCAAGTTTCAGGTTCCCTTGGGCTCT
CCATGCATT

Alignment

ORF - retro_ptro_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.81 %
• Parental protein coverage: 86.63 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNLLPCNPHGNGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVG
          M.LLPCN.H.N.LLY.GF.QDHGC.AC.MENGF.VYNT.PLK.KEKQ.FL.G.VGH.EMLF.CNYLALV.
Retrocopy MILLPCNSHSN*LLYTGFSQDHGCLACWMENGF*VYNTNPLK*KEKQKFLGGRVGHYEMLFCCNYLALVV

Parental  GGKKPKYPPNKVMIWDD-LKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCY
          GGKKPKY.PNKVMI.DD..KKKTV.EIEF.TEVKAVKL.RDRIVVVLDSMIKVF..T.NPHQL..FET..
Retrocopy GGKKPKYLPNKVMI*DD<WKKKTVNEIEFATEVKAVKLQRDRIVVVLDSMIKVFALTQNPHQLYIFETS*

Parental  NPKGLCVLCP-NSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPA-HEGVLSCIALNLQGTRIATASEKG
          NPKGLC.L.....N..L.A.PGTHTGHVQLVD.ASTEKPPVDIPA..EG.LSCI.LNLQGTRIAT...KG
Retrocopy NPKGLCPLSQ>SNNSLL-ALPGTHTGHVQLVDWASTEKPPVDIPA<PEGILSCIILNLQGTRIATTLAKG

Parental  TLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLP
          TL.RIFDTSSGHLIQEL.RGSQAAN..CINF.QD.S.IC.SSDH.TVHIFAAEDP.RNKQS.L.SASFLP
Retrocopy TLLRIFDTSSGHLIQEL*RGSQAANVFCINFSQDESFICISSDHSTVHIFAAEDPGRNKQSNLVSASFLP

Parental  KYFSSKW-SFSKFQVPSGSPCI
          K.FS.K...FSKFQVP.GSPCI
Retrocopy KSFSCKG<GFSKFQVPLGSPCI

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	0.00 RPM	75.52 RPM
SRP007412_cerebellum	0.50 RPM	130.92 RPM
SRP007412_heart	0.00 RPM	43.25 RPM
SRP007412_kidney	0.24 RPM	102.91 RPM
SRP007412_liver	0.33 RPM	85.14 RPM
SRP007412_testis	0.00 RPM	108.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1262 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1262 has 0 orthologous retrocopies within eutheria group .

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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,