RetrogeneDB ID: retro_ecab_413

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:31838547..31839750(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX3X
• Ensembl ID: ENSECAG00000009901
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked [Source:HGNC Symbol;Acc:2745]

Sequence

>retro_ecab_413
TTTGCTGGCTCACACCTGAAGTCTTGAAGTAATCAGAGTGGAGGAAGTACAGCCATCAAGGGGTGTATATTTCTCCTCAC
TTAAGGACAGAGAAGCTACAAAAGGAGTCTACGATGAAGACAGTTCAGGGTGGAATTCTAATAAAGATAAGGGTACCTAG
AGCAGTTCTGAGTCTCATAGTGATTCAAGAGAAAATTCCAGCTTCTTCAGTGATTGTGGAAGTGGATCAAGGGAGAAGTT
TGATGATCGTTGGGAGAGTGACTATGATGGCATTGGCAGTCATGGTGACACAAGTGGCTTTGGCAAATTTGAACGTGGTG
GAAACAGTCACAGTGTAACAAATCAGAGTAAGATGATTGGCCAAAACCACTCTAACCAAGTGAATGCTTGGTACAGGGAC
TTTTTTCAGGAAATAACACTGGGATTAACTTTGAGAAATACAATATTCCAATTGAGGCAATAGGCAACAACTATCCCCCA
CATACTGAAAGTGTCAGTGATGTTGAGATGGGAGAAATTATCATGGGAAACATAAAGCTTATTTGTTATACTCACCTGAC
TCCAGTGCAAAAGGATGCTATGATTATTATCAAAGAGAAAACACGCTTGATGACTTGTACCCAAACAGGGTCTGTAAAAA
CTACAGCATTTCTCTTGCCCATCTTGAGTTAGATTTATTCAGATAGTCCAGGAGAGACTTTGAGGGCCATAAAGGGGAAT
GGAAGGTAGGGGCGCTGCAAACAATCCCTAATATCCTAGGTATTAGCACCAAAGAGAGAATTGGCAGTACCGATCTGTGA
AGAAGCCAGAAAATTTTCCTATCAATCTAGAGTTAGTCCTTACATTGTATATGGTGGTGCTGATATTGGTCAACAGATGT
GTGACTTAGAACATGGATGTCACTTGTTAGTAGCCACTCTAGGAGGCCTAGTAGAAATGAGGTAAAGAGGAAATATTGGA
TAAGACTTCTGAAAATACATGGTGTTGGGTAAAGCTGATCTTATATTGGATGTGAGTTTTGAAGCTCAGATAAGTAGAAA
ATTTAAACAAGTAGTATGCCACCAAAGGAAGTTCTCCACACTATGAGGGTTTAGTGCTACTTTCTCTAAGAAAAATACAG
ACGCTTGCTCATGATTTCTTGGGTGAATATATCTTTTTGGCTGTGGGAAGATTGGCTTTACCTCTGAGAACATCACATAC
AAA

Alignment

ORF - retro_ecab_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 62.29 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FAGLDLNSSDNQSGGSTASKGR-YIPPHLR-NREATKGFYDKDSSGWSSSKDKDAYSSFGSRSDSRGKSS
          FAG..L.S..NQSGGSTA.KG..YI.PHLR..REATKG.YD.DSSGW.S.KDK...SS..S.SDSR..SS
Retrocopy FAGSHLKS*SNQSGGSTAIKGC<YISPHLR<DREATKGVYDEDSSGWNSNKDKGT*SSSESHSDSRENSS

Parental  FFSDRGSGSRGRFDDRGRSDYDGIGSRGDRSGFGKYERGGNSR-WCDKSDEDDWSKPLPPSERLEQELFS
          FFSD.GSGSR..FDDR..SDYDGIGS.GD.SGFGK.ERGGNS...C.KS..DDW.KPL.PSE.L.Q.LFS
Retrocopy FFSDCGSGSREKFDDRWESDYDGIGSHGDTSGFGKFERGGNSH<QCNKSE*DDWPKPL*PSECLVQGLFS

Parental  GGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMA
          G.NTGINFEKY..IP.EA.GNN.PPH.ES.SDVEMGEIIMGNI.L..YT..TPVQK.A..IIKEK..LM.
Retrocopy GNNTGINFEKYN-IPIEAIGNNYPPHTESVSDVEMGEIIMGNIKLICYTHLTPVQKDAMIIIKEKTRLMT

Parental  CAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYR
          C.QTGS.KT.AFLLPILS.IYSD.PGE.LRA.K.NGR.GR.KQ..IS.VLAP.RELAV.I.EEARKFSY.
Retrocopy CTQTGSVKTTAFLLPILS*IYSDSPGETLRAIKGNGR*GRCKQSLIS*VLAPKRELAVPICEEARKFSYQ

Parental  SRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIR
          SRV.P..VYGGADIGQQ..DLE.GCHLLVAT.G.LV.M..RG.IG.DF.KY.VL..AD..LD..FE.QI.
Retrocopy SRVSPYIVYGGADIGQQMCDLEHGCHLLVATLGGLVEMR*RGNIG*DF*KYMVLGKADLILDVSFEAQIS

Parental  RIVEQ-DTMPPKGVRHTMM-FSATFPK-EIQMLARDFLDEYIFLAVGR-VGSTSENITQK
          R...Q...MPPK.V.HTM..FSATF.K..IQ.LA.DFL.EYIFLAVGR..G.TSENIT.K
Retrocopy RKFKQ<SSMPPKEVLHTMR>FSATFSK>KIQTLAHDFLGEYIFLAVGR<IGFTSENITYK

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
SRP021940_articular_cartilage	0.00 RPM	217.70 RPM
SRP021940_cerebellum	0.00 RPM	134.35 RPM
SRP021940_embryo	0.23 RPM	237.75 RPM
SRP021940_placental_villous	0.00 RPM	377.29 RPM
SRP021940_synovial_membrane	0.05 RPM	152.52 RPM
SRP021940_testis	0.19 RPM	87.99 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_413 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_413 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,