RetrogeneDB ID: retro_btau_1824

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:77023091..77023546(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCEE
• Ensembl ID: ENSBTAG00000035247
• Aliases: None
• Description: Methylmalonyl-CoA epimerase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q2KIZ3]

Sequence

>retro_btau_1824
GCATGCATAATGAAGGTGGCTTCAAGTGCTTAGGGCCTTTCCTCAGACTTTAGACTTCAGTTCCAACAGTTAGAACTTCT
TCCACATTGCTGTCCTCGCATCAAGGGGCTGCCCTTATATGGAACCTGAGTCAACTCAATCATGTTGCAGTTTCAGTGCC
AGACTTGTGAAAGGCCAGGTAATTTTATTAGAATGTTCTGGGGCCCAAAGTGGGTGAGCTGGTCCCTTTACCTGAGTATG
GAGTATCTGTCTTTTTTGTCAACCTGGGAAATACCAAGGTGGATCTGCGTCACCCACAGAGAAGCAACAATTCAATTGCA
GGTCTTCTGAATAAAAGCTAGACTGGAGTGGTGCACCCCATCTGCATTGAGGTGGATAATATAAATGCAACTGTGATGGA
TTTGAAAGAAAAGAAGATTCATAATCTAAGTGAAGAGGCCAAAATAGGAGCACAT

Alignment

ORF - retro_btau_1824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.53 %
• Parental protein coverage: 86.86 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARVLKVAAASAAGL-FPRLRTPVSTVRTSASL-SSHPGAGPVWNLGRLNHVAVAVPDLEKARAFYKNVLG
          A...KVA..SA.GL.F.RL.T.V.TVRTS..L.SSH.GA...WNL..LNHVAV.VPDL.KAR.FY.NVLG
Retrocopy ACIMKVAS-SA*GL<FLRL*TSVPTVRTSSTLLSSHQGAALIWNLSQLNHVAVSVPDL*KAR*FY*NVLG

Parental  AEVGEPVPLPEHGVSVVFVNLGNTKMELLHPLGSDSPIAGFLKKNKAGGMHHVCIEVDNINVAVMDLKEK
          ..VGE.VPLPE.GVSV.FVNLGNTK..L.HP..S...IAG.L.K...G..H..CIEVDNIN..VMDLKEK
Retrocopy PKVGELVPLPEYGVSVFFVNLGNTKVDLRHPQRSNNSIAGLLNKS*TGVVHPICIEVDNINATVMDLKEK

Parental  KIRILSEEAKIGAH
          KI..LSEEAKIGAH
Retrocopy KIHNLSEEAKIGAH

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	30.93 RPM
ERP005899_muscle	0.00 RPM	22.86 RPM
SRP017611_brain	0.00 RPM	4.39 RPM
SRP017611_kidney	0.00 RPM	27.62 RPM
SRP017611_liver	0.00 RPM	22.12 RPM
SRP030211_testis	0.00 RPM	3.27 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1824 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035247	1 retrocopy	retro_btau_1824 ,