RetrogeneDB ID: retro_ecab_1000

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:74295047..74295423(-)
• Located in intron of: ENSECAG00000007050

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_1000
TTAGAGGAAAGAAATATAGAAATACTGCAGATGGAGGATGAGAGAGAGCTAAGACTAAAAAAACATGAAGAAATTCTCCA
AGAAATATCCAACTCAATAAGGAATTGCAACATAAGGATTATAAGCATTCCAGAGAAAGGGAGAATGGAGCAGAAAACTT
GTTCCAAGAAATAATAGCTAAAAACTTCCCAAACCTGGGGAAGGAGCTGGAATTACACGTAAATGAAGCTAACAGAACTC
CTAATTACAACAATGTAAAAGACCTTCTCCAAGGCATCTATTAGTAAAGCTGCCAAAAAGAAATGACAGACGAAAAATAT
TAAGAGCAGCAAGGCACAAGAAAGTAACTTACAAAGGAACCCCTATCAGGCTTTCA

Alignment

ORF - retro_ecab_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.83 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEDRNTEMLKMEEERELRLKRSEDIFQEIYNPIRKRNIRIISIPTGE-ERQNRRESLFKEIITENFLNLG
          LE.RN.E.L.ME.ERELRLK..E.I.QEI.N.I..RN..I..I...E.ER.N..E.LF.EII..NF.NLG
Retrocopy LEERNIEILQMEDERELRLKKHEEILQEISNSI--RNCNIRIISIPE<ERENGAENLFQEIIAKNFPNLG

Parental  KGLEIQVKEANRTPNYINV-ERPSPRHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLS
          K.LE..V.EANRTPNY.NV..RPSPRH.LVKL.K......I...AAR.KK.TYKG.PIRLS
Retrocopy KELELHVNEANRTPNYNNV<KRPSPRHLLVKLPKRNDRRKIL-RAARHKKVTYKGTPIRLS

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_1000 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1000 has 0 orthologous retrocopies within eutheria group .

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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,