RetrogeneDB ID: retro_pabe_3657

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:71584440..71585462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX3X
• Ensembl ID: ENSPPYG00000020257
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked [Source:HGNC Symbol;Acc:2745]

Sequence

>retro_pabe_3657
CCTCAACAAGAGAATTGGCTGTACAGATATGAGGAAGCCAGAAAATTTTCATACCAGTCTAGAGTTCATCCTTGTGTAGT
TTATGGTGATGCTGATATTGGTCAGCAAATTCAGGTCTTAGAACATGGATGCCACTTGTTAGTAGCCACGCCAGGACACC
TAGTGGATTTGATGGAAAGAGGAACGATTGGATTAGACTTCTGCAAATACTTAGTGTTGGATGAAGCTGATGGAATGTTG
GATATGGGATTTGGACCTCAGATACATCTTATACTTGAACAAGATACTATGCCACTGAAGGGCATTCATCACATCATGAT
GTTTAGTGCTACTTTTCCTAACGAAATATAGATGCTTGCTCGTGACTTTTTGGATGAATATATCTTTTTTGGCTGTAGGC
AGAGTAGGCTCTACCTCTGAGAATATCACACAGGAAGTAGTTTGGGTGGAAGAGCCAGATAAACGGTCATTTCTGCTTGA
TCTCTTAAATGCACCAGGGAAGGATTCACTGACTTTAGTGTTTGTGGAGACCAAAAAGGGAGCAGATTCTCTGGAGAATT
TCTTATACCATGAAGTATATCCTTGTACTAGTATTCATGGAGACCAATCACAGAGAGATCGAGAAGGAGGCCCTTCATCC
GTTTTGCTTGGGGAAAAATCCCAATTCTAGTGGCTACAGCTGTGGCAGCATGAAGACTAGACATTTCAAATGTGAAACAT
GCTTCAATTTTGATTTGCCAAATGATATTGAAGAATATGTGCCTTGTATTGGCTGTACAGGCTGTGTGGGAATCCAGGGC
CTTGCCACCTCATTCTTTAATGAAAGAAATATGAATATTACAAAGGATTTGTTGGATATTCTTACAGAAGCTAAACAAGA
AGTGCCTGCTTGGTTGGAAAATAAAGCTTATAAACACCACTACAAGGGTGCTATTCGTGCATGATCTAAAAGATTCAGCG
GAGGATTTGGTGCCAGAGACTATTGACAAAGTAGTGGTTCCAGCAGTTCTGGCTTCAGTAGT

Alignment

ORF - retro_pabe_3657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.35 %
• Parental protein coverage: 51.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKY
          P..E.....YEEARKFSY.SRV.PCVVYG.ADIGQQI..LE.GCHLLVATPG.LVD.MERG.IGLDFCKY
Retrocopy PQQENWLYRYEEARKFSYQSRVHPCVVYGDADIGQQIQVLEHGCHLLVATPGHLVDLMERGTIGLDFCKY

Parental  LVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYI-FLAVGRVGSTS
          LVLDEAD.MLDMGF.PQI..I.EQDTMP.KG..H.MMFSATFP.EI.MLARDFLDEYI.FLAVGRVGSTS
Retrocopy LVLDEADGMLDMGFGPQIHLILEQDTMPLKGIHHIMMFSATFPNEI*MLARDFLDEYI>FLAVGRVGSTS

Parental  ENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE-
          ENITQ.VVWVEE.DKRSFLLDLLNA.GKDSLTLVFVETKKGADSLE.FLYHE.Y.CTSIHGD.SQRDRE.
Retrocopy ENITQEVVWVEEPDKRSFLLDLLNAPGKDSLTLVFVETKKGADSLENFLYHEVYPCTSIHGDQSQRDRE>

Parental  EALH-QFRSGKSPILVATAVAARGLDISNVKHV-INFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN
          EALH..F..GK.PILVATAVAA..LDISNVKH...NFDLP.DIEEYV..IG.TG.VG..GLATSFFNERN
Retrocopy EALH>RFAWGKIPILVATAVAA*RLDISNVKHA<FNFDLPNDIEEYVPCIGCTGCVGIQGLATSFFNERN

Parental  INITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSS
          .NITKDLLD.L.EAKQEVP.WLEN.AY.HHYKG..R..SK..RFSGGFGARDY.QSSG.SSS.FSS
Retrocopy MNITKDLLDILTEAKQEVPAWLENKAYKHHYKGAIRA*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	0.06 RPM	139.11 RPM
SRP007412_cerebellum	0.12 RPM	173.28 RPM
SRP007412_heart	1.17 RPM	114.60 RPM
SRP007412_kidney	2.19 RPM	164.74 RPM
SRP007412_liver	1.38 RPM	135.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3657 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3657 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 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,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898, retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657 ,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,