RetrogeneDB ID: retro_pabe_3571

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:10223802..10224842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WEE1
• Ensembl ID: ENSPPYG00000003494
• Aliases: None
• Description: WEE1 homolog (S. pombe) [Source:HGNC Symbol;Acc:12761]

Sequence

>retro_pabe_3571
ACACAGCAGTTTCAGGAGCTGCAGACAATTGCTCTGGAGGTTTTGGTTCTGTGTGTACTGTGTGAAGAGGCAGGATGGAT
GCATGCACCGCATTAGGTGATCAGAAAAGCCTTAGGCCAATTCTACAGTGAGCAAAGCGCTCTGAGAGGAGCACAGGCTC
TACTGCAGTGCCTGGACGGCTTCCTCATGCAGTTCCATATTTCTCTGCCTGGGCAGAAGATGGTGCTATGCTTACACAGG
ATGAATATTGTCATAGTGTAAGTTTAGCTGATGCTGAAGTGAAAACTGCAGAATCATGAGTTACTTCAAAGAAGCAGAGT
TGAAGGGTCTCCTTTTGCAAGGTAGCAGGCGCTTGACCTATATTCATTCAATGTCTTTGGTTCACAGGGATACAAAATCT
AGTAGTATTTTTACATCTCGAGTCTCAATCCCAGATGCTGCCTCTGAAGAAGAGGAAGATGACTGGGGATCCAACAAAAT
TATGTTAAACACAGGTGATCTTGGACGTGTAAGAAGGATCTCTAGTCCACAGTTTGAAGAGGGTGATAGTCATTTTCCTG
CAAATGAAGTTTTACAGGAGGATTATACCCATCTATACAGAGAGAGATTTTTTCACTTGTCCTCACCGTGGTATGTGCTG
CTGGTGCTGAAGCTCTTCCCGGAAATGAAGACCAGCGCATGAATTCACACAGGCCAGGTGACCTTGATAGCACAAGTGCT
TTCCTGAGAGTTTATGGAGTTGAGAAAGGTTATGATTCCTCCAGATCCAGAGAGAAGACCTTCAGCAATGGTCCTGGTAA
GCATTTGGTACTGCTGTCTGCTTCTAGAAAGAGGACAGAACAGTAACAAATAGAATTAAAGCCTGGAAATTTCAAAAATT
TACTTTTAGAAGAATAACTCAAGGAAGCACAGATGGCAAAGGCTGCAGCTGAAGAGGAGCACTGTGATGGCAGGACAGCC
ACCGTGTCCAACACCCAGAGTAATGGGCCATTCAGCCTAGTGGAATGCAAATGAGCTGCTCCATCAACCTTCCTGCATAC

Alignment

ORF - retro_pabe_3571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 54.33 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  TTEFHELEKIG-SGEFGSVFK-CVKRLDGCIYAIKRSKKPLAGSVDEQ-NALREVYAHAVLGQHSHVVRY
          T..F.EL..I..SG.FGSV...CVKR.DGC...I..S.KP.A.S........R.....AV.G...H.V.Y
Retrocopy TQQFQELQTIA<SGGFGSVCT<CVKRQDGCMHRIR*SEKP*ANSTVSK>RSERSTGSTAVPGRLPHAVPY

Parental  FSAWAEDDHMLIQNEYCNGGSLADAI-SENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSN
          FSAWAED..ML.Q.EYC...SLADA..SEN.RIMSYFKEAELK.LLLQ..R.L.YIHSMSLVH.D.K.S.
Retrocopy FSAWAEDGAMLTQDEYCHSVSLADAE<SENCRIMSYFKEAELKGLLLQGSRRLTYIHSMSLVHRDTKSSS

Parental  IFISRTSIPNAASEEGDEDDWASNKVIFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPK-ADI
          IF.SR.SIP.AASEE..EDDW.SNK.....GDLG.V.RISSPQ.EEGDS.F.ANEVLQE.YTHL.....I
Retrocopy IFTSRVSIPDAASEE-EEDDWGSNKIMLNTGDLGRVRRISSPQFEEGDSHFPANEVLQEDYTHLYR<REI

Parental  FALALTVVCAAGAEPLPRNGDQ-WHEIRQGRLP-RIPQVLSQEFTELLKVMIHPDPERRPSAMALV-KHS
          F.L.LTVVCAAGAE.LP.N.DQ..HE..Q.R.P..I.QVLS.EF.EL.KVMI.PDPERRPSAM.LV.KH.
Retrocopy FSLVLTVVCAAGAEALPGNEDQ<AHEFTQAR*P<LIAQVLS*EFMELRKVMIPPDPERRPSAMVLV<KHL

Parental  VLLSASRKSAEQLRIELNAEKFKNSLLQKELKKAQMAKAAAEERALFTDRMATRSTTQSNRTSRLI-GKK
          VLLSASRK..EQ..IEL....FKN.LL...LK.AQMAKAAAEE......R.AT.S.TQSN....L..G..
Retrocopy VLLSASRKRTEQ*QIELKPGNFKNLLLEE*LKEAQMAKAAAEEEHC-DGRTATVSNTQSNGPFSLV<GMQ

Parental  MNRSVSLTIY
          M..S..L..Y
Retrocopy MSCSINLPAY

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	1.77 RPM
SRP007412_cerebellum	0.00 RPM	23.96 RPM
SRP007412_heart	0.00 RPM	7.83 RPM
SRP007412_kidney	0.00 RPM	5.97 RPM
SRP007412_liver	0.00 RPM	4.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3571 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000003494	1 retrocopy	retro_pabe_3571 ,
Pongo abelii	ENSPPYG00000018066	1 retrocopy	retro_pabe_684,