RetrogeneDB ID: retro_ecab_564

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:11374042..11374535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000018840
• Aliases: None
• Description: None

Sequence

>retro_ecab_564
AGAAAAAGCAACATAAGGAAAATGGGTATCCGAGAAGGAGAAGAGAGGGAAAAAAGACCAGAGAGTTTATTTAAAGAAAT
AATAGCTGAGAATTTCCTAAACCTGGAGAAGAAACTGGATATAAAAGTACATGAGCTAATGGCACTCCCAATTATCTCAA
TGCAAAAAGACCTTCTCCAGGGCACATTATATTAAAACTGTCAAAAGCCAATGAGAAAGAAAGAAAATTAACAGTGGCCA
GAGAGAGGAAACTAACATAAAAGGAACCCCCATAAGGCTATCAGTGGATTTCTCAGCAGAAACTACAGGCTACGAGAGAG
TGGAATGATATATTCAAAATATTGGAAGATAAAAACTGTCAGCTAAGAATACTCTATTCAGTAATGCTATCCTTCAGAAA
TGAAGGAGAAATAAAGGCTTTCCCAGACAAACAAAAGCTGAAGGAGTTCATCACATTAGACCAGCCTTACAAGAAATGTT
GAAAGGAGCCCTC

Alignment

ORF - retro_ecab_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.94 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKRNIRIISIPTGEERQNRRESLFKEIITENFLNLGKGLEIQVKE-ANRTPNYINVERPSPRHILVKLAK
          RK.NIR...I..GEER..R.ESLFKEII.ENFLNL.K.L.I.V.E.AN.TPNY.N..RPSP.HI..KL.K
Retrocopy RKSNIRKMGIREGEEREKRPESLFKEIIAENFLNLEKKLDIKVHE<ANGTPNYLNAKRPSPGHIILKLSK

Parental  LVMKEYIMAEAARQKKIT-YKGSPIRLSADFS-QTVQTRREWNDIIKILKYKNYPPRILYPVKLSFRYGR
          ...KE......AR..K.T..KG.PIRLS.DFS.Q..Q..REWNDI.KIL..KN...RILY.V.LSFR...
Retrocopy ANEKERKLT-VARERKLT<IKGTPIRLSVDFS>QKLQATREWNDIFKILEDKNCQLRILYSVMLSFRNEG

Parental  EIKAFQDKQKLREFIT-TRPPLQEMMKTAL
          EIKAF.DKQKL.EFIT..RP.LQEM.K.AL
Retrocopy EIKAFPDKQKLKEFIT<IRPALQEMLKGAL

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_564 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_564 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018840	28 retrocopies	retro_ecab_1000, retro_ecab_1011, retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327, retro_ecab_424, retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545, retro_ecab_564 , retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908, retro_ecab_928, retro_ecab_929,