RetrogeneDB ID: retro_btau_875

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:72589722..72590563(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000019464
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.53009
• Ensembl ID: ENSBTAG00000020338
• Aliases: None
• Description: T-complex protein 1 subunit zeta-2 [Source:RefSeq peptide;Acc:NP_001029814]

Sequence

>retro_btau_875
AAGAGTACAAAGGAGAGAGAGAAATTAGTGAAAGCTGAAAGGAAATTCATCGAAGACAGAGTTAAAAAAATAATCGACCT
GAAAAAGAAAGTCTGTGTTGATTCAGATAAAGGATTTGTTGTTATTAGTCAAAAGGGAATTGATCCCTTTTCCTTAGATG
CTCTTGCCAAAGAAGGCATAATAGCTCTGCGCAGAGCTAAAAGGAGAAACATGGAAAGGCTGACTCTTGCTTGTGGCGGG
ATAGCCCTAAATTCTCTTAATGACCTAAATCCTGATTGTTTGGGACATGCAGGACTTGTCTATGAATATACATTGGGAGA
AGAGAAGTTCACCTTTATTGAGAGATGTAACAATCCTCGCTCTGTCACATTATTGATCAAAGGACCAAATGAGCACACGT
TTACTCAAATCGAAGATGTCATAAGAGATGGCTTGAGGGCTGTTTAAAATGCTACTGATGATGGCTGTTAGTCCCAGGTG
CTGGCGCAGTGGACGTGCAATGGCAGAAGCCCTGGTTAAATACATGCCCAGTGTAAAGGGCAGGGCCCAGCTTGGAGTTC
AAGCATTTGCTGATGCATTGCTCATTATTCCCAAGGTTCTCGCTCAGAACTCTGGTTTTGACCTTCAGGAAACACTAGTT
AAAATTCAAGCAGAACATTCAGAATCCAGTCAGCTTGTGGGTGTGGACTTGAACACTGATGAACCAATGGTAGCAGCAGA
AGCAGGCATATGGGATAAGTACTGTGTAAAGAAACAGCTTCTTCACTCCTGCACTGTGATTGCCACCAACATTCTCCTGG
TTGATGAGATCATGAGAGCTGGAATGTCTTCTCTAAAAGGT

Alignment

ORF - retro_btau_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 52.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTAEEKEKLVKAERKFIEDRVQKIIDLKDKVCAQSNKGFVVINQKGIDPFSLDALAKHGILALRRAKRRN
          K...E.EKLVKAERKFIEDRV.KIIDLK.KVC..S.KGFVVI.QKGIDPFSLDALAK.GI.ALRRAKRRN
Retrocopy KSTKEREKLVKAERKFIEDRVKKIIDLKKKVCVDSDKGFVVISQKGIDPFSLDALAKEGIIALRRAKRRN

Parental  MERLSLACGGVAVNSVEDLSVDCLGHAGLVYEYTLGEEKYTFIEDCINPRSVTLLVKGPNKHTLTQIKDA
          MERL.LACGG.A.NS..DL..DCLGHAGLVYEYTLGEEK.TFIE.C.NPRSVTLL.KGPN.HT.TQI.D.
Retrocopy MERLTLACGGIALNSLNDLNPDCLGHAGLVYEYTLGEEKFTFIERCNNPRSVTLLIKGPNEHTFTQIEDV

Parental  VRDGLRAIKNAIEDGC-VVPGAGAVEV-AIAEALVTYKHTIQGRARLGVQAFADALLIIPKVLAQNSGYD
          .RDGLRA..NA..DGC..VPGAGAV.V.A.AEALV.Y.....GRA.LGVQAFADALLIIPKVLAQNSG.D
Retrocopy IRDGLRAV*NATDDGC<LVPGAGAVDV<AMAEALVKYMPSVKGRAQLGVQAFADALLIIPKVLAQNSGFD

Parental  LQETLVKVQAEHSNSKQPVGIDLNTGEPMVAADAGVWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSS
          LQETLVK.QAEHS.S.Q.VG.DLNT.EPMVAA.AG.WD.YCVKKQLLHSCTVIATNILLVDEIMRAGMSS
Retrocopy LQETLVKIQAEHSESSQLVGVDLNTDEPMVAAEAGIWDKYCVKKQLLHSCTVIATNILLVDEIMRAGMSS

Parental  LKG
          LKG
Retrocopy LKG

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	0.50 RPM	2.16 RPM
ERP005899_muscle	2.38 RPM	0.69 RPM
SRP017611_brain	3.20 RPM	1.19 RPM
SRP017611_kidney	3.67 RPM	1.84 RPM
SRP017611_liver	2.64 RPM	0.38 RPM
SRP030211_testis	2.70 RPM	143.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_875 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_875 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020338	1 retrocopy	retro_btau_875 ,
Canis familiaris	ENSCAFG00000018298	1 retrocopy	retro_cfam_342,