RetrogeneDB ID: retro_ptro_3130

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:73938610..73939629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX3Y
• Ensembl ID: ENSPTRG00000022488
• Aliases: None
• Description: Pan troglodytes DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked (DDX3Y), mRNA. [Source:RefSeq mRNA;Acc:NM_001008986]

Sequence

>retro_ptro_3130
CCCCAACAAGAGAATTGGCTGTACAGATATGAGGAAGTCAGAAAATTTTCATACCAGCCTAGAGTTCATCCTTGTGTAGT
TTATGGTGATGCTGATATTGGTCAGCAAATTCAGGTCTTAGAACATGGATGCCACTTGTTAGTAGCCACGCCAGGACGTC
TAGTGGATTTGATGGAAAGAGGAAAGATTGGATTAGACTTCTGCAAATACTTAGTGTTGGATGAAGCTGATAGGATGCTG
GATATGGGATTTGGACCTCAGATACATCTTATACTTGAACAAGACACTATGCCACTGAAGGGCATTCATCACATCATGAT
GTTTAGTGCTACTTTTCCTAACGAAATACAGATGCTTGCTCGTGACTTTTTGGATGAATATATCTTTTTGGCTGTAGGCA
GAGTAGGCTCTACCTCTGAGACTATCACACAGGAAGTAGTTTGGGTGGAAGAGCCAGATAAACGGTCATTTCTGCTTGAT
CTCTTAAATGCACCAGGGAAGGATTCACTGACTTTAGTGTTTGTGGAGACCAAAAAGGGAGAAGATTCTCTGGAGAATTT
CTTATACCATGAAGTATATCCTTGTACTAGTATTCATGGAGACCAATCACAGAGAGATCGAGAAGGAGGCCCTTCATCAG
TTTTGCTTGGGGAAAATCCCAATTCTAGTGGCTACAGCTGTGGCAGCATGAAGACTAGACATTTCAAATGTGAAACATGC
TTCAATTTTGATTTGCCAAGTGATATTGAAGAATATGTGCCTTGTATTGGCTGTACAGGATGTGTGGGAATCCAGGGCCT
TGCCACCTCATTTTTAATTAAAGAAATATGAATATTACAAAGGATTTGTTGGATATTCTTATAGAAGCTAAACAAGAAGT
GCCTGCTTGGTTGGAAAATAAAGCTTATAAACACCACTACAAGGGTGGTATTCATGCATGATCTAAAAGATTCAGTGGAG
GATTTGGTGCCAGAGACTATTGACAAAGTAGTGGTTCCAGCAGTTCTGGCTTCAGTAGT

Alignment

ORF - retro_ptro_3130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.84 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKY
          P..E.....YEE.RKFSY..RV.PCVVYG.ADIGQQI..LE.GCHLLVATPGRLVD.MERGKIGLDFCKY
Retrocopy PQQENWLYRYEEVRKFSYQPRVHPCVVYGDADIGQQIQVLEHGCHLLVATPGRLVDLMERGKIGLDFCKY

Parental  LVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSE
          LVLDEADRMLDMGF.PQI..I.EQDTMP.KG..H.MMFSATFP.EIQMLARDFLDEYIFLAVGRVGSTSE
Retrocopy LVLDEADRMLDMGFGPQIHLILEQDTMPLKGIHHIMMFSATFPNEIQMLARDFLDEYIFLAVGRVGSTSE

Parental  NITQKVVWVEDLDKRSFLLDILGAAGTDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE-E
          .ITQ.VVWVE..DKRSFLLD.L.A.G.DSLTLVFVETKKG.DSLE.FLYHE.Y.CTSIHGD.SQRDRE.E
Retrocopy TITQEVVWVEEPDKRSFLLDLLNAPGKDSLTLVFVETKKGEDSLENFLYHEVYPCTSIHGDQSQRDRE>E

Parental  ALHQFRSGKSPILVATAVAARGLDISNVRHV-INFDLPSDIEEYVHRIGRTGRVGNLGLATSF-FNEKNI
          ALHQF..GK.PILVATAVAA..LDISNV.H...NFDLPSDIEEYV..IG.TG.VG..GLATSF.FN..N.
Retrocopy ALHQFCLGKIPILVATAVAA*RLDISNVKHA<FNFDLPSDIEEYVPCIGCTGCVGIQGLATSF<FN*RNM

Parental  NITKDLLDLLVEAKQEVPSWLENMAYEHQYKGGSRGRSKSNRFSGGFGARDYRQSSGSSSSGFGA
          NITKDLLD.L.EAKQEVP.WLEN.AY.H.YKGG....SK..RFSGGFGARDY.QSSGSSSSGF..
Retrocopy NITKDLLDILIEAKQEVPAWLENKAYKHHYKGGIHA*SK--RFSGGFGARDY*QSSGSSSSGFSS

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	0.41 RPM	40.29 RPM
SRP007412_cerebellum	0.18 RPM	49.04 RPM
SRP007412_heart	0.06 RPM	56.11 RPM
SRP007412_kidney	0.24 RPM	68.36 RPM
SRP007412_liver	0.03 RPM	26.12 RPM
SRP007412_testis	0.32 RPM	323.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3130 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130 ,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,