RetrogeneDB ID: retro_btau_1853

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:122038365..122039877(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF8
• Ensembl ID: ENSBTAG00000005796
• Aliases: DCAF8, H326, WDR42A
• Description: DDB1- and CUL4-associated factor 8 [Source:RefSeq peptide;Acc:NP_001193348]

Sequence

>retro_btau_1853
TACCAGTTAGGAAAGCCGGGAAAGGAAGGAGAAGTGAAGGAAGCATTGGCACAAGAAAAGTGGCCTCAGGTACAGTGCCG
TGAGGCTAATCAAGCCCAAGCCCAGTATTTATATGCCAAGGATTGGGCCCTGGAGGAACGGGTAGCTTCCGAGATATCCA
CCCTCCCCAACCCACGTTGGAAAGTCCTGAATGCTCTTCGAGAGCGGCAGCTGGGTTCAAGTGCCCACTTTGTGTATGAG
GCCTGTGGGGCAAGAGTCTTTGTGCAGCATTTCCACCTGCAGTATTGGCTTGCAGGCCACAATGTTTGTGTTAACACTGT
GCACTTTAACCAGTGTGGCACCTGGCTGGCCACTAGCAGTGATGACCTGAAAGTGATATTGTGGGACTGGGTGCATCGGC
AGCCAGTACTGGAGTTTGAGAGTGGTCACAGAAATAATGTTTAGCAGGCCAAGTTCCTTCCCCACTGTGGTGATACCACC
CTGGCCATGTGTGGCTGCGATGGGCAGATCTGCATAGCCGAGCTGTCTGCTCTCCCACACTGCGGGAAAACTAAATGTGT
GGCCCAGCACAGGGGAGCCTCCCACAAGTTGGGTCTGGATCCTGACTCCCCTTTTAAGTTCCTCACTTCAGGTGAAGATG
CAATTGTCTTTGCCATTGATCTCAGACAAGGCCAGCCGGCTTCAAAAGTGGTGGTAACCAGAGAGAAGGAGAAGAGAGTG
GGGCTGTATTCGATCTATGTGAATCCTGCCAATAATTACCATTTTGCAGTGGGCGGATGAGATCAGTTTGTAAGAATTTA
TGACCAGAGGAAGATTAATTAGAGTGATAATAATGGAGTGCTCAAGAAATTTTGTCCTCATCACCTACCCAACTGTGATG
CTAAAGCTCACATTACCTGCCTTGTGTACAGTCACAATGGCACAGAGCTCCTGGCCAGTTACAATGATGAGGATATTTAC
CTCTTCAAGTCCTCTCATGTTGATGGAGCCCAATATGTGAAAAGACACAAGGGGCACAGAAATAATGCCACAGTCAAAGG
TGTCAATTTCTACGGTCCCAGAAGTGAGTTCATCATGAGTGGCAGTGATTGCGGGCACATCTTCTGGGAGAAGTCATCCT
GCCAGATTGTTCAGTACATGGAAGGGGATAAAGGAGGGACTATTAACTGTATTGAAGCCCATCCTTACCTACCTGTGATG
GCGACCAGCGGCCTAGACCGCAATGCTAAGATCTGGGTACCCACAGCTAAAGTTATCACTTGCCTTGCTGGCTTAAACAG
TGTGATTAAGAGGAACAAGCAGGGACGAGATAAAGACAGAAAGCACCATACTCATCTGTTCGAAAGCCATATGCTTTGGT
TCCTCATGCATCACCTGACACAGAGAGGACATTGCCCGCAGTAGGGAGCTACTGGAATCGAGGTGGTGGAAACCAACTCA
GATGAGTCTTCCAGTACCTCAGATGTGTCGGAGGAGGAAGAGAACCAAGACTGTGTGCAGTGCCTGCTATCC

Alignment

ORF - retro_btau_1853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.53 %
• Parental protein coverage: 85.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSVNDESQVHDRSEEEEEEEHPRRRVQRKRANRDQDSSDDERALEDWVSSETSALPRPRWQALPALRERE
          Y............E....E..P............Q.......ALE..V.SE.S.LP.PRW..L.ALRER.
Retrocopy YQLGKPGKEGEVKEALAQEKWPQVQCREANQAQAQYLYAKDWALEERVASEISTLPNPRWKVLNALRERQ

Parental  LGSSARFVYEACGARVFVQRFRLQHGLEGHTGCVNTLHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFE
          LGSSA.FVYEACGARVFVQ.F.LQ..L.GH..CVNT.HFNQ.GTWLA..SDDLKV..WDWV.RQPVL.FE
Retrocopy LGSSAHFVYEACGARVFVQHFHLQYWLAGHNVCVNTVHFNQCGTWLATSSDDLKVILWDWVHRQPVLEFE

Parental  SGHKSNVFQAKFLPNSGDSTLAMCARDGQVRVAELSATQCCKNTKRVAQHKGASHKLALEPDSPCTFLSA
          SGH..NV.QAKFLP..GD.TLAMC..DGQ...AELSA...C..TK.VAQH.GASHKL.L.PDSP..FL..
Retrocopy SGHRNNV*QAKFLPHCGDTTLAMCGCDGQICIAELSALPHCGKTKCVAQHRGASHKLGLDPDSPFKFLTS

Parental  GEDAVVFTIDLRQDRPASKLVVTKEKEKKVGLYTIYVNPANTHQFAVGGRDQFVRIYDQRKIDENENNGV
          GEDA.VF.IDLRQ..PASK.VVT.EKEK.VGLY.IYVNPAN...FAVGG.DQFVRIYDQRKI....NNGV
Retrocopy GEDAIVFAIDLRQGQPASKVVVTREKEKRVGLYSIYVNPANNYHFAVGG*DQFVRIYDQRKIN*SDNNGV

Parental  LKKFCPHHLVNSESKANITCLVYSHDGTELLASYNDEDIYLFNSSHSDGAQYIKRYKGHRNNATVKGVNF
          LKKFCPHHL.N...KA.ITCLVYSH.GTELLASYNDEDIYLF.SSH.DGAQY.KR.KGHRNNATVKGVNF
Retrocopy LKKFCPHHLPNCDAKAHITCLVYSHNGTELLASYNDEDIYLFKSSHVDGAQYVKRHKGHRNNATVKGVNF

Parental  YGPKSEFVVSGSDCGHIFLWEKSSCQIIQFMEGDKGGVVNCLEPHPHLPVLATSGLDHDVKIWAPTAETS
          YGP.SEF..SGSDCGHIF.WEKSSCQI.Q.MEGDKGG..NC.E.HP.LPV.ATSGLD...KIW.PTA...
Retrocopy YGPRSEFIMSGSDCGHIF-WEKSSCQIVQYMEGDKGGTINCIEAHPYLPVMATSGLDRNAKIWVPTAKVI

Parental  TELTGLKDVIKKNKRERDEDSLHHTDLFDSHMLWFLMHHLRQRRHHRRWREPGVGATDADSDESPSSSDT
          T.L.GL..VIK.NK..RD.D..HHT.LF.SHMLWFLMHHL.QR.H.......G.......SDES.S.SD.
Retrocopy TCLAGLNSVIKRNKQGRDKDRKHHTHLFESHMLWFLMHHLTQRGHCPQ*GATGIEVVETNSDESSSTSDV

Parental  SDEEEGPDRVQCMPS
          S.EEE..D.VQC..S
Retrocopy SEEEENQDCVQCLLS

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	12.26 RPM
ERP005899_muscle	0.00 RPM	29.72 RPM
SRP017611_brain	0.00 RPM	76.42 RPM
SRP017611_kidney	0.00 RPM	93.06 RPM
SRP017611_liver	0.00 RPM	35.34 RPM
SRP030211_testis	0.14 RPM	55.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1853 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1853 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_223
Mus musculus	retro_mmus_111

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853 ,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,