RetrogeneDB ID: retro_btau_43

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:108331611..108332157(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000011783
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BRP44L
• Ensembl ID: ENSBTAG00000027879
• Aliases: BRP44L, MPC1
• Description: Mitochondrial pyruvate carrier 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCG2]

Sequence

>retro_btau_43
ATGGCAGCGGTGGTGGCTCTGTGCCGGAAGGCGATGGAGACCGTGAAGACTAAGGAGTTCCGAGATTACCTGGCCAGCAC
GCACTTCTGGGGTCCAGTGGCCAACTGGGGCCTCCCGCTGGCTGCCTTCAGGGACATGAGGGCATCACCGGACATCATCA
GTGGCCGCATGACGACTGCACTCATCTTCTACTCGATGGCCTTCATGCGCTTCGCCTACCGTGTACAGCCTCGCAATTTG
CTGCTGATGGCGTGTCACGGCACCAACATAGTGGCACAGAGTATGCAGGCGGGCCGCTACCTGAATTACCACTATGGCGG
TGGCACCACGGCAGCCACCACTGCTGCTGTCTCTGCCGCTTCTGCCACCTCTACCGGCTCTGTGGATTCTTCTGCCACCT
CTACCGGCTCTGTGGATTCTTCTGCCACCTCTACCGGCTCTGTGGATTCTACTGCAGCTACCACCCCTGCAGCTGAAGAC
CCTGTGGCTCACAGCAACTGCCAGGAGATCACCTGCTGTTATCTAGTGACCTGGGACTGTGATTGA

Alignment

ORF - retro_btau_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 89.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKV
          AL.RKA...V..K.FRDYL.STHFWGPVANWGLP.AA..DM..SP.IISGRMT.AL..YS..FMRFAY.V
Retrocopy ALCRKAMETVKTKEFRDYLASTHFWGPVANWGLPLAAFRDMRASPDIISGRMTTALIFYSMAFMRFAYRV

Parental  QPRNWLLFACHATNEVAQLIQGGRLIRH
          QPRN.LL.ACH.TN.VAQ..Q.GR....
Retrocopy QPRNLLLMACHGTNIVAQSMQAGRYLNY

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	102.81 RPM
ERP005899_muscle	0.05 RPM	46.67 RPM
SRP017611_brain	0.05 RPM	15.49 RPM
SRP017611_kidney	0.06 RPM	230.92 RPM
SRP017611_liver	0.00 RPM	120.21 RPM
SRP030211_testis	8.75 RPM	24.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_43 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_43 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43 ,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,