RetrogeneDB ID: retro_btau_579

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:43633306..43633854(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000000426
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COMMD8
• Ensembl ID: ENSBTAG00000001348
• Aliases: None
• Description: None

Sequence

>retro_btau_579
ATGGACCCGGAAGAAGGGACACCCTTGTGGCGGCTGCAGAAGCTTCCCACAGAGCAGGGCCTGCAGCTTCTTCACAAAAT
AATTGATGGCACTTGTGGCCGAACTTATCCTCTCTACCAGGATTATCACAGGATTTGGGATTCAGCAGAATGGATGCATG
TTCTAGAAGACATTACCACCTTTTTCAGAGCTGTAGTTGGTAAAAATTTATCTGACGAAGAGATATCTCAGCAGTTGAAT
CAGCTGAATTCATCTCATCAAGAAGCTATCATGAAATGCTTAAAAAGTAGGAAAGATGAAATCAAGCAGACTCTGTTGGA
AGAAACAGTTGATATTTCCTCTGCACAGCTACAGAATTTTGATTGGCAGTTAAAGCTTACACTTCCTAGTGACAAGATTG
CTATATTACAAATGCCACTTTTAAACATTCATCTAGATGTAAAAGAAAAAGGTGAAGTCAAGCCATATTCTGTTGAAATG
AGTAAAGAAGAGCTGAAAATCTAATAAATTCCTGGGAAGCAGCTAACAAGGTGGTCCTGCAGTTGAAA

Alignment

ORF - retro_btau_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPEEGTPLWRLQKLPAERGLQLLHKIIDGICGRTYPLYQDYHSVWDSTEWMHVLEDITTFFKAVVGKNL
          M.PEEGTPLWRLQKLP.E.GLQLLHKIIDG.CGRTYPLYQDYH..WDS.EWMHVLEDITTFF.AVVGKNL
Retrocopy MDPEEGTPLWRLQKLPTEQGLQLLHKIIDGTCGRTYPLYQDYHRIWDSAEWMHVLEDITTFFRAVVGKNL

Parental  SDEEISQQLNQLNSSHQEAIMKCLKSRKDEIKKTLLEEIVDISSARLQDFDWQIKLALSSDKIASLQMPL
          SDEEISQQLNQLNSSHQEAIMKCLKSRKDEIK.TLLEE.VDISSA.LQ.FDWQ.KL.L.SDKIA.LQMPL
Retrocopy SDEEISQQLNQLNSSHQEAIMKCLKSRKDEIKQTLLEETVDISSAQLQNFDWQLKLTLPSDKIAILQMPL

Parental  LNLYLDVKENGEVKPYSVEMSKEEL-QKLINSLEAANKVVLQLK
          LN..LDVKE.GEVKPYSVEMSKEEL...LINS.EAANKVVLQLK
Retrocopy LNIHLDVKEKGEVKPYSVEMSKEEL<ENLINSWEAANKVVLQLK

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	0.07 RPM	3.75 RPM
ERP005899_muscle	0.00 RPM	6.81 RPM
SRP017611_brain	0.00 RPM	11.37 RPM
SRP017611_kidney	0.00 RPM	15.71 RPM
SRP017611_liver	0.00 RPM	3.55 RPM
SRP030211_testis	0.02 RPM	12.14 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_579 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001348	1 retrocopy	retro_btau_579 ,
Echinops telfairi	ENSETEG00000020257	3 retrocopies	retro_etel_1416, retro_etel_182, retro_etel_210,
Felis catus	ENSFCAG00000023811	1 retrocopy	retro_fcat_421,
Myotis lucifugus	ENSMLUG00000011376	1 retrocopy	retro_mluc_1158,
Macaca mulatta	ENSMMUG00000021777	1 retrocopy	retro_mmul_434,
Ochotona princeps	ENSOPRG00000000739	1 retrocopy	retro_opri_805,
Ictidomys tridecemlineatus	ENSSTOG00000001221	1 retrocopy	retro_itri_1566,