RetrogeneDB ID: retro_btau_662

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:39208175..39208772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1B
• Ensembl ID: ENSBTAG00000004085
• Aliases: None
• Description: Histone chaperone ASF1B [Source:UniProtKB/Swiss-Prot;Acc:Q17QJ0]

Sequence

>retro_btau_662
ATGGCTAAGGTGTCAGTATTGAACATGGCGGTGCTGGAAAATCTGAGCCTTTTCCACAGCCCTTTCTGGTTGAGACATCA
GCTTCGAGTGCAATGAGGCCCTGGCAGACTACCTGGAGTGGAAGAACGTTTATATTGGCTCAGCTGAGAGTGAATTTGAT
CAAATCCTAGACTCTGCTGGTTGGCCCTGTCCTGGCAGGGAGACACATGTTCATCTTTCAGGCAGATTCCCCCAACCCAT
CCCTCATCCTCGAGTCTGATAGCCTGGGAGTGACCATGGTCCTCATCACCTGCAGCTACCACAGACAGGAGTTCATCCGA
GTCAGCTACAGCGTCGACAGTGGGTACCTTAGCAGCTAGCTGTGCGAGAACCCACCCCTGAAGTCACACTTCTCTCAGCT
CCAGTGGAACATCTTGGCCTCAGATCCCCTGGTGAACTGCTTCCACATCAACTGGGACAACAACACAGACAGGTTGGAAG
CCATAGAGAACCAGGACCCTGCCCTGGGCTGCTGTCTCCCCCTCAGCTGCACAGGTACCCTTGGGTCTCCCTGGCTGCGT
AATGGGCCTCCTCCCTCAGAATTCCATGGACTTCATC

Alignment

ORF - retro_btau_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAKVSVLNVAVLENPSPFHSPFRF-EISFECNEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVP-AG
          MAKVSVLN.AVLEN.S.FHSPF....ISFECNEALAD.LEWK..Y.GSAES.EFDQILDS....P.P.AG
Retrocopy MAKVSVLNMAVLENLSLFHSPFWL>DISFECNEALADYLEWKNVYIGSAES-EFDQILDSA-GWPCP>AG

Parental  RHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLSPELRENPPLKPDFSQLQRN
          RHMF.FQAD.PNPSLI.E.D..GVT.VLITC.YH.QEFIRV.Y.V...YLS..L.ENPPLK..FSQLQ.N
Retrocopy RHMFIFQADSPNPSLILESDSLGVTMVLITCSYHRQEFIRVSYSVDSGYLSS*LCENPPLKSHFSQLQWN

Parental  ILASNPRVTRFHINWDNNMDRLEAIENQDSSLGCGLPLSCTPIKGLGLP-SCIPGLLPENSMDCI
          ILAS.P.V..FHINWDNN.DRLEAIENQD..LGC.LPLSCT....LG.P..C..GLLP.NSMD.I
Retrocopy ILASDPLVNCFHINWDNNTDRLEAIENQDPALGCCLPLSCTGT--LGSP>GCVMGLLPQNSMDFI

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	0.87 RPM
ERP005899_muscle	0.00 RPM	9.08 RPM
SRP017611_brain	0.00 RPM	1.51 RPM
SRP017611_kidney	0.00 RPM	1.30 RPM
SRP017611_liver	0.00 RPM	0.60 RPM
SRP030211_testis	0.00 RPM	59.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_662 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_662 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004085	1 retrocopy	retro_btau_662 ,
Canis familiaris	ENSCAFG00000016482	1 retrocopy	retro_cfam_33,
Echinops telfairi	ENSETEG00000013713	1 retrocopy	retro_etel_379,
Myotis lucifugus	ENSMLUG00000000537	4 retrocopies	retro_mluc_1426, retro_mluc_2042, retro_mluc_2614, retro_mluc_775,
Monodelphis domestica	ENSMODG00000012099	4 retrocopies	retro_mdom_366, retro_mdom_367, retro_mdom_369, retro_mdom_688,
Sorex araneus	ENSSARG00000000534	1 retrocopy	retro_sara_552,