RetrogeneDB ID: retro_btau_1218

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:34114950..34115298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNHIT3
• Ensembl ID: ENSBTAG00000012672
• Aliases: None
• Description: Zinc finger HIT domain-containing protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q2KIH1]

Sequence

>retro_btau_1218
GAGCAGTGCAAGCCTGCAACTGATCTTGTTGAGAAAAAAATAAGATCAGCTCTTACTGCAAAAACTAAAAAGTGTGGAAA
ATGAAGATGATGATGATGACTCTGTAGCTGATTTTCTCAATAGTGATGAGAAGAGGATAGAGTGTCTTTGCAGAATTTAA
AGAGTTTAGGGGAGTCTGCAGCGCTGAGGAGCTTACTGCTCAAGCCGCACCTCAGACAGTTGATGGTTGACCTCAATCAG
GCGGACGACAAGGCCAAGCTTATGCAGGCCTGCATGCAGGAACCCTTGTTTGTGGAGTTTGAGGACTGCTGCTTGAGTAT
CGTGGAGCCATCTTAGAACAAGGATCCT

Alignment

ORF - retro_btau_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.34 %
• Parental protein coverage: 66.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQCRPAAGPVE-KKIRSALTAKTKKPVENEGSLDDDDSVADFLNSDE-EEDRVSLQNLKNLGESAALRSL
          EQC.PA...VE.KK....L..K.K..VENE...DDDDSVADFLNSDE.EEDRVSLQNLK.LGESAALRSL
Retrocopy EQCKPATDLVE>KK*DQLLLQKLKS-VENED--DDDDSVADFLNSDE<EEDRVSLQNLKSLGESAALRSL

Parental  LLNPHLRQLMVDLDQADDKAKLMRACMQEPLFVEFADCCLSIVEPSQNEDP
          LL.PHLRQLMVDL.QADDKAKLM.ACMQEPLFVEF.DCCLSIVEPS.N.DP
Retrocopy LLKPHLRQLMVDLNQADDKAKLMQACMQEPLFVEFEDCCLSIVEPS*NKDP

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	6.85 RPM
ERP005899_muscle	0.00 RPM	13.25 RPM
SRP017611_brain	0.00 RPM	12.84 RPM
SRP017611_kidney	0.00 RPM	11.56 RPM
SRP017611_liver	0.00 RPM	9.21 RPM
SRP030211_testis	0.04 RPM	12.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1218 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1218 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012672	1 retrocopy	retro_btau_1218 ,
Dasypus novemcinctus	ENSDNOG00000011745	1 retrocopy	retro_dnov_1037,
Echinops telfairi	ENSETEG00000018407	1 retrocopy	retro_etel_1415,
Myotis lucifugus	ENSMLUG00000013155	1 retrocopy	retro_mluc_1100,
Macaca mulatta	ENSMMUG00000007918	1 retrocopy	retro_mmul_938,