RetrogeneDB ID: retro_btau_1031

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:32970343..32970805(-)
• Located in intron of: ENSBTAG00000021902

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.62681
• Ensembl ID: ENSBTAG00000036297
• Aliases: None
• Description: putative ribosome-binding factor A, mitochondrial [Source:RefSeq peptide;Acc:NP_001106721]

Sequence

>retro_btau_1031
AGGAAGTTTTGGTATGAAGGTCCTTCCTTGGGCTCTCACTTGACCCACAAGCCATCCCAGTTGGAGTTCTTGATGAAGAG
CACCACCAGGAGAACCCGAAGGAAGACCGGGGCACCTGAAGGCGCTGAACATTCTCCTCTACAAAGCGCTCACAGGCTTG
CTATGCACCCCGGAAGTGAGCCAGGACCTGTGCGACCCGAACGCGGAGCTCTGCAAGGTCTCTCTGGCTTCAGGCTTCTC
TGCCTGCCGCGTCTTCTGGAGGGCGACCCTCTCTGAGGCCCAGAACGCACACCGGAGGCTGTCCTGCAGAGGAGTGCTGC
GCACATGGGGCATCTTCTGATGTCCCAGCAGACCCCGAGGAACGTGCCGCCCAGAGTGTGTGTTCAGGACAAAAAATACG
TAGCTATGGTGGAGATTGATCGGCTACTGGCAATTGCTGATTTTGGACCCCGGGATGACAAG

Alignment

ORF - retro_btau_1031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 53.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKFWYEGPSLGSHLTHKSSQLEFLTKSTSRRTR-KEDQV-RLRALNGLLYKALTDLLCTPEVSQELCDLN
          .KFWYEGPSLGSHLTHK.SQLEFL.KST.RRTR.KED....L.ALN.LLYKALT.LLCTPEVSQ.LCD.N
Retrocopy RKFWYEGPSLGSHLTHKPSQLEFLMKSTTRRTR<KEDRG<HLKALNILLYKALTGLLCTPEVSQDLCDPN

Parental  VELCKVSLTSDFSACRVFWRATLSEAQNAH-TEAVLRRSAAHMRHLLMSQQTLRNVPPIVFVQDKKYAAV
          .ELCKVSL.S.FSACRVFWRATLSEAQNAH..EAVL.RSAAHM.HLLMSQQT.RNVPP.V.VQDKKY.A.
Retrocopy AELCKVSLASGFSACRVFWRATLSEAQNAH<PEAVLQRSAAHMGHLLMSQQTPRNVPPRVCVQDKKYVAM

Parental  MEVDRLLAIADFGPRGEK
          .E.DRLLAIADFGPR..K
Retrocopy VEIDRLLAIADFGPRDDK

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	1.87 RPM
ERP005899_muscle	0.00 RPM	13.46 RPM
SRP017611_brain	0.00 RPM	5.76 RPM
SRP017611_kidney	0.12 RPM	15.94 RPM
SRP017611_liver	0.08 RPM	7.02 RPM
SRP030211_testis	0.00 RPM	7.56 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1031 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1031 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036297	1 retrocopy	retro_btau_1031 ,
Cavia porcellus	ENSCPOG00000000170	1 retrocopy	retro_cpor_911,
Equus caballus	ENSECAG00000008292	1 retrocopy	retro_ecab_146,
Pan troglodytes	ENSPTRG00000010137	1 retrocopy	retro_ptro_1062,