RetrogeneDB ID: retro_btau_274

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:105901478..105902302(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000011051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C10H15ORF23
• Ensembl ID: ENSBTAG00000032340
• Aliases: None
• Description: putative TRAF4-associated factor 1 [Source:RefSeq peptide;Acc:NP_001033144]

Sequence

>retro_btau_274
CAGGCGGCAGACGCGGTCGGTGGTACGGCAGTTATTGCCAAGCATCTTTTGAACCAGAGCGACGAGGCATGCGGGCAGGA
GCAGCAGGCACCTGGGCCCCAGTCGTGCTGCCTCGTTACGATGACCAGCGTGGTTAAGACAGTGTACACCCTGCAGCCCT
CCTTTGCGCTGAGCAGCGGTCTGCCCGCAGATGCACAAACTCGAGCCACTTTTAAGAGCCAGTTACCTGTTAAGTCCAAA
GAGGTTGATGTTTCCAGACCACATTCAGGAGCTTCAGAGAATGATGTTACAAAAATCATCAAACCGAGACATGAGAATGG
GCAGGTGAAGGCTACAGACACCTCCAGGAGGAACCTCAGGAAGAGCTACAAACCATTGAGTAAACAGAAATCGGAAGAAG
AGCTCAAGGATAAGAACCAGCTCTTAGAGGCTGTCAACAAGCAGTTGCACCAGAAATTGATTGAAACTCAGGGAGAGCTG
AAGGACCTGACTCAAAAAGTAGAGCTGCTGGAGAAGTTTCAGGACAACAGTTTGGCAATTTTAGAAAGCAAAGCCTCAAC
CCAGGCAGTGAGACCCTGGCATCACAGCAAGACTCCACCGCAGATCACATGGACTCCATGCTGCTGTTACAAACTTTACA
AGATGAACTGAAGCTTTTTAACGAAACAGCCAAAAAGCAGATGGAGGAGTTACAGGCCTTAAAGGTAAAGTTGAAGATGA
AAGAAGAAGAGAGAGCCCAGTTCCTTGAACAACAGACCTTATGTAGCAGTCAAGTAAATGATTTCACAACAGCCCTTGAG
GAAATGGAGCAGCTATTAGAAATA

Alignment

ORF - retro_btau_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 87.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAADAVGGTAVIAEHLLNQSDEACGQEQQAPGPQPCRLVTMTSVVKTVYTLQPSCVLSSGLPADAQTRAT
          QAADAVGGTAVIA.HLLNQSDEACGQEQQAPGPQ.C.LVTMTSVVKTVYTLQPS..LSSGLPADAQTRAT
Retrocopy QAADAVGGTAVIAKHLLNQSDEACGQEQQAPGPQSCCLVTMTSVVKTVYTLQPSFALSSGLPADAQTRAT

Parental  FKSQLPVKSKEVDVSRPHSGASENDVTKIIKPRRENGQVKATDTSRRNLRKSYKPLSKQKSEEELKDKNQ
          FKSQLPVKSKEVDVSRPHSGASENDVTKIIKPR.ENGQVKATDTSRRNLRKSYKPLSKQKSEEELKDKNQ
Retrocopy FKSQLPVKSKEVDVSRPHSGASENDVTKIIKPRHENGQVKATDTSRRNLRKSYKPLSKQKSEEELKDKNQ

Parental  LLEAVNKQLHQKLIETQGELKDLTQKVELLEKFQDNCLAILESK-GLNPGSETLASQQDSTADHVDSMLL
          LLEAVNKQLHQKLIETQGELKDLTQKVELLEKFQDN.LAILESK..LNPGSETLASQQDSTADH.DSMLL
Retrocopy LLEAVNKQLHQKLIETQGELKDLTQKVELLEKFQDNSLAILESK<SLNPGSETLASQQDSTADHMDSMLL

Parental  LQTLQDELKLFNETAKKQMKELQALKVKLKMKEEERAQFLEQQTLCSNQVNDFTTALEEMEQLLEI
          LQTLQDELKLFNETAKKQM.ELQALKVKLKMKEEERAQFLEQQTLCS.QVNDFTTALEEMEQLLEI
Retrocopy LQTLQDELKLFNETAKKQMEELQALKVKLKMKEEERAQFLEQQTLCSSQVNDFTTALEEMEQLLEI

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	3.46 RPM
ERP005899_muscle	0.05 RPM	13.57 RPM
SRP017611_brain	0.00 RPM	4.34 RPM
SRP017611_kidney	0.00 RPM	4.33 RPM
SRP017611_liver	0.00 RPM	0.91 RPM
SRP030211_testis	0.26 RPM	247.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_274 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_274 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032340	2 retrocopies	retro_btau_1217, retro_btau_274 ,
Choloepus hoffmanni	ENSCHOG00000007085	3 retrocopies	retro_chof_1378, retro_chof_2237, retro_chof_504,
Monodelphis domestica	ENSMODG00000000464	1 retrocopy	retro_mdom_1200,
Otolemur garnettii	ENSOGAG00000009825	1 retrocopy	retro_ogar_1829,
Tupaia belangeri	ENSTBEG00000012043	4 retrocopies	retro_tbel_2696, retro_tbel_3958, retro_tbel_4092, retro_tbel_787,
Tursiops truncatus	ENSTTRG00000010577	1 retrocopy	retro_ttru_240,