RetrogeneDB ID: retro_ecab_1058

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:36840426..36841076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM4
• Ensembl ID: ENSECAG00000024971
• Aliases: None
• Description: glutathione S-transferase mu 4 [Source:HGNC Symbol;Acc:4636]

Sequence

>retro_ecab_1058
GCCGTAATCTTGGGTTACTGGGACATCCATGGGCTGGCTCATATAGTGCACCCGTTTCTGGAATACACAGACTCAAACTA
TGAGGAAAAGAACTACATGATGAGGGATACTCCTGCCTATGACAGAAGCCAGTGGCTAAAAGAAAAATTCAAGCTGGGCC
TGGACTTTCCCAATCTTCCTTACTTAATTCATGAGGCTCACAAGATCACCTAGAGCAATGCCATCCTTCACTACATTGCT
TGAAGCACAACCTACAAGGGGGGACAGAAGAAGGAAAGACTCATGTAGACATTTTGGAGAACTAGGTTACACACATCCCC
AGTCAGCTGGCCAGTGTCTCCTACAGCCCTGATTTCGAGACACTGAAGCCTGAGTGCTTGGATGGGCTCCCTGAAAATAT
GAAGCTCTTTTCACAGTTTCTGGGGAAAAGGTCATGGTTTGCATGGGACAAGATCACCTTTGTGGATTTCCTCACTTATG
ACATCCTTGACCTGCACCGTATATTTGAGCCTGAGTGCCTGAATGCATTTCCAAATGTGAGAGACTTCATCACCTGATTA
GAGGGCCTAAAGAAGTTATCTGCCTACGTTAAGTGCAGCCGCCTCTTCCCTCGATCTGTGTACATAATGATTGCCATGTG
GGGTAACAAG

Alignment

ORF - retro_ecab_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.56 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMTLGYWDIRGLAHAIRLLLEYTDSNYEEKKYTMGDAPDYDRSQWLSEKFKLGLDFPNLPYLIDGAHKIT
          A..LGYWDI.GLAH.....LEYTDSNYEEK.Y.M.D.P.YDRSQWL.EKFKLGLDFPNLPYLI..AHKIT
Retrocopy AVILGYWDIHGLAHIVHPFLEYTDSNYEEKNYMMRDTPAYDRSQWLKEKFKLGLDFPNLPYLIHEAHKIT

Parental  QSNATL-YIA-RKHNLCGETEEEKIRVDILENQLMDTCNQLARVCYSPDFEKLKPEYLEALPETMKLFSQ
          .SNA.L.YIA..KHNL.G.TEE.K..VDILEN.......QLA.V.YSPDFE.LKPE.L..LPE.MKLFSQ
Retrocopy *SNAILHYIA<LKHNLQGGTEEGKTHVDILEN*VTHIPSQLASVSYSPDFETLKPECLDGLPENMKLFSQ

Parental  FLGKRPWFAGDKLTYVDFLAYDILDLHRIFEPKCLDAFSNLKDFITRLEGLKKISAYMKSSRFLPSPIYT
          FLGKR.WFA.DK.T.VDFL.YDILDLHRIFEP.CL.AF.N..DFIT.LEGLKK.SAY.K.SR..P...Y.
Retrocopy FLGKRSWFAWDKITFVDFLTYDILDLHRIFEPECLNAFPNVRDFIT*LEGLKKLSAYVKCSRLFPRSVYI

Parental  KIAIWGNK
          .IA.WGNK
Retrocopy MIAMWGNK

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	3.48 RPM
SRP021940_cerebellum	0.00 RPM	47.47 RPM
SRP021940_embryo	0.00 RPM	4.63 RPM
SRP021940_placental_villous	0.05 RPM	22.08 RPM
SRP021940_synovial_membrane	0.00 RPM	7.96 RPM
SRP021940_testis	0.19 RPM	8.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1058 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1058 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_2062

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058 ,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,