RetrogeneDB ID: retro_ecab_694

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:20728439..20729423(-)
• Located in intron of: ENSECAG00000011891

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSECAG00000016504
• Aliases: None
• Description: glutamic-oxaloacetic transaminase 2, mitochondrial [Source:HGNC Symbol;Acc:4433]

Sequence

>retro_ecab_694
ATGGCCTTGCAGTGCTCTGGCTGCATCCTGTCTGGGGTCCTGCCGCCCTCCACCCAGGCCTCGCTGTGGCAGCCTCTGCC
AGATCCATCTCAGTGGGAGATGGGACCCCCAGATCCCATCCTAGGAGTCACAGGAATCTGTAAGAGAGACACCAACAGCA
AAAAGATGAATCTAGGAGGTGGTGCCTACTGCGATGATAGTGGAAAGCCTTACATGATCCCTAGCTTCCGGAAGGCAGAG
GCCCAGATTGGTGCAAAAAAAATGGACAAAGAATACCTGTCCATTGTGAGACTGGCTGAATTTTGTAAGGTTTCTGCAAA
ATTAGCCCTGGGTGAGAACAGCAGAGTGCTGAAAAGTGACCAGTATGTCACTGTGCAGACCATTTCTGGAACTGAGGCCC
TAAGGACCGCAGCCAGTTTTCTGCAAAGATTTTTAAAGTTCAGCCGAGATGTCTTTCTGCCCAAACATCCTGGGAAAATC
ATACACCCATCCTCAGGGACGCTGGATGCAGCTACATGGTTATTGATACTGTGACCCCAAGACTTGTAGCTTTGACTTCA
CAGTGCTATGAAGGACACTTTAAAAATGCCAGAGCAAAGTGTTTTTCTCCTGCATGACCATGTCCACAATCCCAGGCGAG
TGGACCCTCATTCTAAGCAGTGGAAGGAAATAGCAACGGTAGTGAGGAAACAGAATCTCTTTTCGTTCTTTGAAGTGGCC
TACCAAGGCTTTGCCGGTGGTGATGGTAACAAGGATGCCTGGGCAGTGCGCCACTTCATTGAAGAGGGCATTAATATTTG
TCTCTTCCAATCCTTTGCCAAGAACGTGGACTTATATGGTGACTGTGTGGGAGCCTTCACTGTGGTCTGCGAAGATGCTG
ATGAAGCCAAAAGGGGGGAGTGACAGTTGAAGATCTTGATCCGTTCCACGTATTCCAACCCTCTTCTCAAAGGGGCCCGG
ATTGCCTCAACCATTCTGACAGCT

Alignment

ORF - retro_ecab_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.41 %
• Parental protein coverage: 77.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MALLHSGRVLSGVA-SAFHPGLAAAASARA-SSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYR
          MAL..SG..LSGV...A.HPGLA.AASAR..S.W....EMGPPDPILGVT...KRDTNSKKMNLG.GAY.
Retrocopy MALQCSGCILSGVL<AALHPGLAVAASARS>SQW----EMGPPDPILGVTGICKRDTNSKKMNLGGGAYC

Parental  DDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIGGLAEFCKASAELALGENSEALKSGRYVTVQSISGTGAL
          DD.GKPY..PS.RKAEAQI.....DKEYL.I..LAEFCK.SA.LALGENS..LKS..YVTVQ.ISGT.AL
Retrocopy DDSGKPYMIPSFRKAEAQIGXXXXDKEYLSIVRLAEFCKVSAKLALGENSRVLKSDQYVTVQTISGTEAL

Parental  RIGANFLQRFFKFSRDVFLPK-PSWGNHTPIFRDAG-LQLHAYRYYDPKTCGFDVT-GALEDISKIPQQS
          R..A.FLQRF.KFSRDVFLPK..SW.NHTPI.RDAG..QLH.Y.Y.DPKTC.FD.T..A..D..K.P.QS
Retrocopy RTAASFLQRFLKFSRDVFLPK<TSWENHTPILRDAG<MQLHGY*YCDPKTCSFDFT<SAMKDTLKMPEQS

Parental  IILLHACAHNPTGVDPRPEQWKEIATLVKKNNLFAFFDMAYQGFASGDGDKDAWAVRYFIEQGINVCLCQ
          ..LLH...HNP..VDP...QWKEIAT.V.K.NLF.FF..AYQGFA.GDG.KDAWAVR.FIE.GIN.CL.Q
Retrocopy VFLLHDHVHNPRRVDPHSKQWKEIATVVRKQNLFSFFEVAYQGFAGGDGNKDAWAVRHFIEEGINICLFQ

Parental  SYAKNMGLYGERVGAFTMVCKDADEAKRVESQLKILIRPLYSNPPLNGARIASTILTS
          S.AKN..LYG..VGAFT.VC.DADEAKR.E.QLKILIR..YSNP.L.GARIASTILT.
Retrocopy SFAKNVDLYGDCVGAFTVVCEDADEAKRGE*QLKILIRSTYSNPLLKGARIASTILTA

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	0.06 RPM	51.12 RPM
SRP021940_cerebellum	0.05 RPM	165.09 RPM
SRP021940_embryo	0.08 RPM	126.23 RPM
SRP021940_placental_villous	0.34 RPM	116.77 RPM
SRP021940_synovial_membrane	0.16 RPM	56.33 RPM
SRP021940_testis	0.06 RPM	49.43 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_694 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694 ,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,