RetrogeneDB ID: retro_btau_1846

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:102792755..102793873(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX3X
• Ensembl ID: ENSBTAG00000035907
• Aliases: None
• Description: ATP-dependent RNA helicase DDX3X [Source:RefSeq peptide;Acc:NP_001179891]

Sequence

>retro_btau_1846
TTTTCTGGAGGCAACACTGGGGTTAACTTTGAAAATTTTGAGGACATTCCAGTTGGAGCAACAGGCAACAATGGTCCTCC
ACACAGTGAAAGTTTCAGTGATGTTAGATGGGAGAAATTATTATGGGAAACATTGAGCTTACTCATCACACTCACCCAAC
TCCAGTGCAAAAGCATGCTATTCCTATTATCAAAGAGAAGAGTGACCTGATGGCCTGTCCCCAAACAGGGTCTGGGAAAA
CTGCAGCATTTCTCTTGCCCATCTTGAGTCAGATTTATTTTGTGGGTCCAGGCCAGGCTCTGAGGGCCATGAAGGAAAAT
GGAAGATATGGGTGCTGCAAACAATACCCAATCTCTTTGGTGTTAGTGCCAACTAGAGAATTGGCCATATAGATCTATGA
GGAAGCCAGGAAATTTTCATACCAATCTAGAGTTTGTCCTTGTGTGGTTTATGGTGGTGCTGATATTGGTCAGCAAATTT
TAGACTTAGAACGTGGATGCCATTTGTTAGTTACCACTCTAGGAAGTCTAGTGGATATGATGGAAAGAGGGAAAATTTGA
TTAGACTTCTGCAAATAGTTGGTGTTAGGTGAAGCTGATCAGATGTTGGATATGGGGTTTGAATCTCAAATACATAGAAT
CATTGAACAAGATATGCCACCAAAGGGAGTTCACCACACTATGAAGTTTAGTGCTACCTTCCCTAAGGAAATACAGATGC
TTGCTCATGATTTCTTGGATGAATATATCTTTTTGGCCATAGGAAGAGTTGGCTCTCCCTCTGAAAACATCACACAGAAA
GTAGTTTGGGTGGAAGAGTCAGACAAACAGTCATTTCTGCTTGACCTTCTAAATGCAACAGGCAAAGATTCACTGACCTT
ATTGTTTGTGGAGACCAAAAAGGGTGCAAATTCTCTAGAGGATTTCTTAGACCATGAAGGATATGCTTGTACCAGTTTCC
ATGCAGACCAATCTCAGAGAGATAGAGAAGAGGCACTTTACCAGTTCTGCTCAGGTAAAAGCCCGATTCTCATGGCTACA
ATAGTAGCAGCAAGAGGACTGGACATATCAAACATGAAACATGTTATCAATTTTGACTTGCCAAGTGATATTGAAGAA

Alignment

ORF - retro_btau_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 56.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVE-MGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRD
          FSGGNTG.NFE...DIPV.ATGNN.PPH.ESFSDV..MGEIIMGNIELT..T.PTPVQKHAIPIIKEK.D
Retrocopy FSGGNTGVNFENFEDIPVGATGNNGPPHSESFSDVR<MGEIIMGNIELTHHTHPTPVQKHAIPIIKEKSD

Parental  LMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKF
          LMAC.QTGSGKTAAFLLPILSQIY..GPG.ALRAMKENGRYG..KQYPISLVL.PTRELA..IYEEARKF
Retrocopy LMACPQTGSGKTAAFLLPILSQIYFVGPGQALRAMKENGRYGCCKQYPISLVLVPTRELAI*IYEEARKF

Parental  SYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEP
          SY.SRV.PCVVYGGADIGQQI.DLERGCHLLV.T.G.LVDMMERGKI.LDFCK.LVL.EAD.MLDMGFE.
Retrocopy SYQSRVCPCVVYGGADIGQQILDLERGCHLLVTTLGSLVDMMERGKI*LDFCK*LVLGEADQMLDMGFES

Parental  QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRS
          QI.RI.EQD.MPPKGV.HTM.FSATFPKEIQMLA.DFLDEYIFLA.GRVGS.SENITQKVVWVEESDK.S
Retrocopy QIHRIIEQD-MPPKGVHHTMKFSATFPKEIQMLAHDFLDEYIFLAIGRVGSPSENITQKVVWVEESDKQS

Parental  FLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA
          FLLDLLNATGKDSLTL.FVETKKGA.SLEDFL.HEGYACTS.H.D.SQRDREEAL.QF.SGKSPIL.AT.
Retrocopy FLLDLLNATGKDSLTLLFVETKKGANSLEDFLDHEGYACTSFHADQSQRDREEALYQFCSGKSPILMATI

Parental  VAARGLDISNVKHVINFDLPSDIEE
          VAARGLDISN.KHVINFDLPSDIEE
Retrocopy VAARGLDISNMKHVINFDLPSDIEE

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
ERP005899_liver	0.00 RPM	66.04 RPM
ERP005899_muscle	0.00 RPM	107.37 RPM
SRP017611_brain	0.05 RPM	142.98 RPM
SRP017611_kidney	0.12 RPM	238.75 RPM
SRP017611_liver	0.08 RPM	114.77 RPM
SRP030211_testis	0.00 RPM	41.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1846 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1846 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 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,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,