RetrogeneDB ID: retro_btau_407

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:57162265..57162849(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH2B
• Ensembl ID: ENSBTAG00000020149
• Aliases: None
• Description: Ribonuclease H2 subunit B [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBI3]

Sequence

>retro_btau_407
TTTTCAAGGAAAAAAAATTATTGGTTTATAAATGAATCAGTTCAAGCAAGAGGTCTTCTTCACTTTGCCACACCTATGGA
CTCTCTGTTTCTACTTCTCCACTACCTTATAATGGCCAGTAAAGAGGTGAAGTTTCAGCCCCTGGATCAAGTTGTGATGG
ATGACGTGTTCCCGGATTGCAACTTGTTGCTGAAACTTCCTGAACTTGAGAAGTTATAGACACGTGACAGAGGAGAAAGA
AATAGACAAGAAGAAATACTACAAGAACAGCAAAGAGAAGACATTAAAATGATTAGGAAAAAAAAGGTTAATGAGAAAAT
GGCAGCATTAAAAACCAATAAGGTAAATGTCAGTGCCAGGGTACAGTCTATTGCGTTTTTCTCTAGTGACCAGGTTTCCA
GTGCCAAGGACGAGTATTATGTCCATTATGCCCATGGTCTGATATCTGATCCATCCCTAAACAATAAAGTGATAACTTAT
CTAAATATTTAAAGCTTCCAGAACCTCCAGCTTCAGTGCCAAACCCTCCATAGAAGAAAACAAAGTTATCAGACAAGCCT
GTAGAAGCGAAAGAAGATTACACT

Alignment

ORF - retro_btau_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.34 %
• Parental protein coverage: 64.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKEKNHSWFINESVQSGGLLHFATPVDPLFLLLHYLIKADKESFQGKFQPLDQVVMDDMFPDCILLLKLP
          F......WFINESVQ..GLLHFATP.D.LFLLLHYLI.A.KE....KFQPLDQVVMDD.FPDC.LLLKLP
Retrocopy FSRXXXYWFINESVQARGLLHFATPMDSLFLLLHYLIMASKEV---KFQPLDQVVMDDVFPDCNLLLKLP

Parental  ELEKLLQHVTEEKEVDKKKYYKYSKEKTLKWLGKKVNQTMAALKTNKVNVSARVQSTAFFSGGQVSSDKD
          ELEKL......E.............E.........VN..MAALKTNKVNVSARVQS.AFFS..QVSS.KD
Retrocopy ELEKL*TRDRGERNRQEEILQEQQREDIKMIRXXXVNEKMAALKTNKVNVSARVQSIAFFSSDQVSSAKD

Parental  EDYVRYAHGLISD-YIPKQLSDDLSKYLKLPEPPASVRNPPSKKAKLSDEPVMAKEDYT
          E.YV.YAHGLISD..IPKQ.SD.LSKYLKLPEPPASV.NPP.KK.KLSD.PV.AKEDYT
Retrocopy EYYVHYAHGLISD<SIPKQ*SDNLSKYLKLPEPPASVPNPP*KKTKLSDKPVEAKEDYT

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	13.77 RPM
ERP005899_muscle	0.00 RPM	10.98 RPM
SRP017611_brain	0.00 RPM	14.34 RPM
SRP017611_kidney	0.00 RPM	12.27 RPM
SRP017611_liver	0.00 RPM	5.29 RPM
SRP030211_testis	0.00 RPM	11.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_407 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020149	1 retrocopy	retro_btau_407 ,
Callithrix jacchus	ENSCJAG00000008585	1 retrocopy	retro_cjac_2249,
Dasypus novemcinctus	ENSDNOG00000010489	1 retrocopy	retro_dnov_2225,
Mus musculus	ENSMUSG00000021932	1 retrocopy	retro_mmus_1752,