RetrogeneDB ID: retro_btau_466

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:28487639..28488428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH1
• Ensembl ID: ENSBTAG00000019295
• Aliases: None
• Description: Malate dehydrogenase, cytoplasmic [Source:UniProtKB/Swiss-Prot;Acc:Q3T145]

Sequence

>retro_btau_466
AACAAAGAAGAGATTGCCTTCAAAGACCTGGATGTGGCCACTCTTATGGGCTCCATGCCAAGAAGGGATGGCATGGAGTG
GAAAGATTTACTCAAAGCAAATATGAAAATCTTCAAATGCCAGGGTGCAGCCTTGGACAAATATGCCAAGAAGTCAGTTA
AGGCTATGGTGGTGGGAAACCCAGCCAATACTAACTGCCTGATTATCTCTAAGTCAGCGCCATCCATCCCGAAGGACAAC
TTCAGTTGCTTGACTCGTTTGGATCACAACCGAGCTAAAGCTCAGACTGCTCTTAAACTTGGAGTGACTTCTGATGATGT
AAAGAATGCCATCATCTGGGGAAACCATTCCTCAACTCAGTATCCAGATGTCAACCATGCCAAGGTAAAACTGCAAGGAG
TGGAAGTTGGTGTTTATGAAGCTCTGAAAGATGACAGCTGGCTCAAGGGAGAATTCATCAGGGCCGTGCAGTAGCATGAT
GCTGCTGTCATCAAGGCGCAGAAACTGCCCAGTGCCACATTAGCTGCAAAAGCCATCTGTGACCACGTCAGATACATCTG
GTTTGGAACCCCAGAGGGAGAGTTTGTGTCCATGGGCATTATCTCTGATGGCAACTCCTATGGTATTCCTGATGATCTCC
TTTACTCGTTCCCTGTTACAATCAAGGATAAGACCTAGAAGGTTGTTGAAGGTCTCCCTATTAATGATTTCTCACGTGAG
AAGATGGATCTTACTGCAAAGGAACCAGCAGAAGAGAAAAAAACTGCATTTGAATTTCTTGCCTCTGCC

Alignment

ORF - retro_btau_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 78.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTAS
          .KEEIAFKDLDVA.L.GSMPRRDGME.KDLLKAN.KIFKCQGAALDKYAKKSVK..VVGNPANTNCL..S
Retrocopy NKEEIAFKDLDVATLMGSMPRRDGMEWKDLLKANMKIFKCQGAALDKYAKKSVKAMVVGNPANTNCLIIS

Parental  KSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYE
          KSAPSIPK.NFSCLTRLDHNRAKAQ.ALKLGVTSDDVKN.IIWGNHSSTQYPDVNHAKVKLQG.EVGVYE
Retrocopy KSAPSIPKDNFSCLTRLDHNRAKAQTALKLGVTSDDVKNAIIWGNHSSTQYPDVNHAKVKLQGVEVGVYE

Parental  ALKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGIP
          ALKDDSWLKGEFI..VQ...AAVIKA.KL.SA..AAKAICDHVR.IWFGTPEGEFVSMGIISDGNSYGIP
Retrocopy ALKDDSWLKGEFIRAVQ*HDAAVIKAQKLPSATLAAKAICDHVRYIWFGTPEGEFVSMGIISDGNSYGIP

Parental  DDLLYSFPVTIKDKTWKVVEGLPINDFSREKMDLTAKELAEEKETAFEFLASA
          DDLLYSFPVTIKDKT.KVVEGLPINDFSREKMDLTAKE.AEEK.TAFEFLASA
Retrocopy DDLLYSFPVTIKDKT*KVVEGLPINDFSREKMDLTAKEPAEEKKTAFEFLASA

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	55.87 RPM
ERP005899_muscle	0.16 RPM	190.94 RPM
SRP017611_brain	0.00 RPM	288.74 RPM
SRP017611_kidney	0.24 RPM	249.36 RPM
SRP017611_liver	0.00 RPM	57.16 RPM
SRP030211_testis	0.06 RPM	32.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_466 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466 ,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,