RetrogeneDB ID: retro_btau_669

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:57487659..57488121(+)
• Located in intron of: ENSBTAG00000022069

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49772
• Ensembl ID: ENSBTAG00000009394
• Aliases: None
• Description: E3 SUMO-protein ligase NSE2 [Source:RefSeq peptide;Acc:NP_001069265]

Sequence

>retro_btau_669
ACAATAAACCATGTAAAAGAAGATGTCCAGAAAAAATATCCAATCTAAAATTATTAATGAAGTTGTTTTTGGCTTTACAG
AATAAGAATTCTGATGTAGACTTTCAAAATAATGAAAAATATGTACAATTTAAACAACAGCTGAAAGAACTAAAGAAGCA
ATATGGTCTTCAAGCAGACAGGATGATGGCACAGAAGGAGCTGATGAAGATGATTGTGACTCAAAGTCAGACCGACTTCA
TCTGCCCCATTTACACACTTGGAAATGAAGAAACCAGTGAAAAATAAAACAGGTGGCCACACCTACAAAGAAGAAGCCAT
TGCTGGCATGATAGAGTCTAAGCACAAAAGGAAGAAAAAGGCCTGTTGCCTGAAAATTGGCTGTAGCCACACAGATGTGA
GAATGTCTGATCTCAGCCAGGAAGAGGTGCTCAGAAGGGCAACTGAAAGCCACAACAAGAAA

Alignment

ORF - retro_btau_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.08 %
• Parental protein coverage: 89.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TINHVKEERS-EKIPDLKLLVEKKFLALQNKNSDADFQNNEKFVQFKQQLKELKKQYGLQSDREADITEG
          TINHVKE....EKI..LKLL..K.FLALQNKNSD.DFQNNEK.V....Q.K...K....Q....AD....
Retrocopy TINHVKEDVQ<EKISNLKLLM-KLFLALQNKNSDVDFQNNEKYV----QFKQQLKELKKQYGLQADRMMA

Parental  VDE--DMIVTQSQTNFICPI-TQLEMKKPVKNKVCGHTYEEEAIVRMIESKHKRKKKACCPKIGCSHVDM
          ..E...MIVTQSQT.FICPI.T.LEMKKPVKNK..GHTY.EEAI..MIESKHKRKKKACC.KIGCSH.D.
Retrocopy QKELMKMIVTQSQTDFICPI>THLEMKKPVKNKTGGHTYKEEAIAGMIESKHKRKKKACCLKIGCSHTDV

Parental  RMSDLIQDEALRRAIESHKKR
          RMSDL.Q.E.LRRA.ESH.K.
Retrocopy RMSDLSQEEVLRRATESHNKK

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	4.04 RPM
ERP005899_muscle	0.00 RPM	5.07 RPM
SRP017611_brain	0.00 RPM	3.43 RPM
SRP017611_kidney	0.06 RPM	4.45 RPM
SRP017611_liver	0.00 RPM	2.42 RPM
SRP030211_testis	0.04 RPM	16.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_669 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669 ,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,