RetrogeneDB ID: retro_ecab_1032

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0003:1225362..1226073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRS2
• Ensembl ID: ENSECAG00000013105
• Aliases: None
• Description: MRS2 magnesium transporter [Source:HGNC Symbol;Acc:13785]

Sequence

>retro_ecab_1032
AAACTTAGCATCTTGCAGCCACTGAGCCTCGAGACACTGGAAGCTTCAGTGGATCCCAAACATCCTTCTGTAGACAGCAA
ACTGCACAGTGTACTACAAAATGGCAAAAGTCTACCAGAGGTAGAAATGGATATTAAAATTTCTAAAGAGTCGCTTTTGG
AGGTCTTGGAGGAAGAGGGGTTGCTGGAAGAGTTCTGTCTGACAAGATGGAGTGACCCGCAAGTCTCTGAAGAGAACCGC
GCTGGGGCTGACGGCACAGAAGATGTGGAGCTGCTGTTGGAACACTGCTACCGAGCGGCTGAGGATCTCCGCAGCGCAGC
CCGCGAACTTCGGGGCTGACTGACGGTTCACAAAGAATTACGTTCTTCAGTCTGGACAGCACCGTAGCGAGATGACGAGG
AGGAGCCTGCAGCTGACCGTGGGAACCTGCTCTGTTCCACTCTGTGGACTAACGGCAGTTGCTTTTGGAGTGAATTTGGA
GTCTTGCCTCGCAGAGGACCGTAGAGTGTCTGGCTGGTTACAGGAATCCCGGTCGTGGGAAGCGGCCTCGTCTGGAGGCG
TTTGCTGTCATTCTTGGACGACAGCTTAAAGCTCCTTTGCCCCCTGGGATGGTCTTTACCTAAAAAGACCCTCCAGGCAG
AGAGAAGGATGGAAACAAAACACAGCTTCCGGCCGGGTGGACTCAGATCAAGCAGGAGCGTCCTCACGCAC

Alignment

ORF - retro_ecab_1032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.84 %
• Parental protein coverage: 62.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLSILQPLILETLEALVDPKHSSVDRSKLHILLQNGKSLSELETDIKIFKESILEILDEEELLEELCLTK
          KLSILQPL.LETLEA.VDPKH.SVD.SKLH..LQNGKSL.E.E.DIKI.KES.LE.L.EE.LLEE.CLT.
Retrocopy KLSILQPLSLETLEASVDPKHPSVD-SKLHSVLQNGKSLPEVEMDIKISKESLLEVLEEEGLLEEFCLTR

Parental  WSDPQVFEKSSTGIDHAEEMELLLENYHRLAEDLSNAAHELRL-LIDDSQSIIFINLDS-HRNVMMRLNL
          WSDPQV.E....G.D..E..ELLLE...R.AEDL..AA.ELR..L.D.SQ.I.F..LDS.HR..M.R..L
Retrocopy WSDPQVSEENRAGADGTEDVELLLEHCYRAAEDLRSAARELRG<LTDGSQRITFFSLDS<HRSEMTRRSL

Parental  QLTMGTFSLSLFGLMGVAFGMNLESSLEEDHRV-FWLITGIMFMGSGLIWRRLLSFLGRQLEAPLPPMVA
          QLT.GT.S..L.GL..VAFG.NLES.L.ED.RV..WL.TGI...GSGL.WRRLLSFL...L...L.P...
Retrocopy QLTVGTCSVPLCGLTAVAFGVNLESCLAEDRRV<VWLVTGIPVVGSGLVWRRLLSFLDDSLKL-LCPLGW

Parental  SLPKKTLQADRRMEVKHSFRPDGLASSRNLLAN
          SLPKKTLQA.RRME.KHSFRP.GL.SSR..L..
Retrocopy SLPKKTLQAERRMETKHSFRPGGLRSSRSVLTH

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
SRP021940_articular_cartilage	0.00 RPM	1.00 RPM
SRP021940_cerebellum	0.00 RPM	3.17 RPM
SRP021940_embryo	0.00 RPM	7.16 RPM
SRP021940_placental_villous	0.00 RPM	2.60 RPM
SRP021940_synovial_membrane	0.00 RPM	1.84 RPM
SRP021940_testis	0.00 RPM	1.73 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1032 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006424	1 retrocopy	retro_dnov_1486,
Equus caballus	ENSECAG00000013105	1 retrocopy	retro_ecab_1032 ,
Homo sapiens	ENSG00000124532	1 retrocopy	retro_hsap_4006,
Gorilla gorilla	ENSGGOG00000009098	1 retrocopy	retro_ggor_2689,
Macaca mulatta	ENSMMUG00000001018	2 retrocopies	retro_mmul_2312, retro_mmul_878,
Pongo abelii	ENSPPYG00000016278	1 retrocopy	retro_pabe_939,
Pan troglodytes	ENSPTRG00000017774	1 retrocopy	retro_ptro_2720,