RetrogeneDB ID: retro_btau_327

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:6181679..6182020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSBTAG00000001137
• Aliases: CLTA, CLTA2
• Description: Clathrin light chain A [Source:UniProtKB/Swiss-Prot;Acc:P04973]

Sequence

>retro_btau_327
CAGACAGAACCTGAAAGTATCCTGTAAAGGACAGAATAGCAAACTGAATGCTTGGAAGCCCTTGATGCCAATTCTTAGAA
GCAGGAAGCAGAGTAGAAAGAAAAAGCCATCAAGGATCTGGACAAGTGGTATGCGAGGCAGGCTGGCAGCTCCAGAAGAC
AAAAGCCAACAACAGGGCAGCGGAAGAAGCCTTTGTACATGACATTGAGGAGTTGTCCCCAGGCACTGAGTGGGAACGGG
CGGCCCAGCTGTGTGACTTTAACCCGAAGTCCAGCAAGCAGGCCAAAGACATCTCCCATGGGCATTCTGTCCTCATCTCC
CTCAAGCAGGGCCCCCTGGTG

Alignment

ORF - retro_btau_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSEPESIRKWREEQTERLEALDANSRKQEAEWKEKAIKELDEWYARQDE-QLQKTKANNRAAEEAFVNDI
          Q.EPESI....E.QTE.LEALDANS.KQEAE.KEKAIK.LD.WYARQ...QLQKTKANNRAAEEAFV.DI
Retrocopy QTEPESIL*RTE*QTECLEALDANS*KQEAE*KEKAIKDLDKWYARQAG<QLQKTKANNRAAEEAFVHDI

Parental  EESSPGTEWERVARLCDFNPKSSKQAKDVSRMRSVLISLKQAPLV
          EE.SPGTEWER.A.LCDFNPKSSKQAKD.S...SVLISLKQ.PLV
Retrocopy EELSPGTEWERAAQLCDFNPKSSKQAKDISHGHSVLISLKQGPLV

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	32.30 RPM
ERP005899_muscle	0.00 RPM	139.47 RPM
SRP017611_brain	0.00 RPM	60.39 RPM
SRP017611_kidney	0.00 RPM	117.24 RPM
SRP017611_liver	0.00 RPM	60.33 RPM
SRP030211_testis	0.01 RPM	39.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_327 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_327 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327 ,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,