RetrogeneDB ID: retro_ecab_142

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:123714474..123714869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000009821
• Aliases: None
• Description: None

Sequence

>retro_ecab_142
GAGAAAAGAGATCAGTGTAATAAAAATATTTTAAGAAAACATTTTCCAAATTTGATGAAAGATATAAACACACAGATTCA
AGAAGCTCAGCAAACATGCAAACAAAATAAATACCAAGAAATCTATGACCAGACACACACTAATAAAATTTTAGAAAACT
GAAGATAAAAATATCTCGAAAGGAACCAGAAAAATTTAGCATTACTTATAGGGGGAAAAGTGTTCAAATGACTGTGAATT
TCTCTTCAGAAAACAAGCAAGCCAGAAGGAAGTGGAACATTTTTAAAGTACTGAAAGAAAAGAACCTTCAACCCAGAATT
CTACATCCAGCAAAAATATTCTTTGGAGATGAAAGTGAAATAAAGATATTCTTAGATGAAGGAAAACTAAGAGAA

Alignment

ORF - retro_ecab_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.11 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EERDKEAENRVAENFPNLKKETDIHIQEAQRTPK-KISPKRATPRHIIIKISKMNDKERIPRAARQK-KI
          E.RD....N.....FPNL.K.....IQEAQ.T.K.KI..K....RH..IK..K..DK..I....R....I
Retrocopy EKRDQCNKNILRKHFPNLMKDINTQIQEAQQTCK>KINTKKSMTRHTLIKF*KTEDKN-ISKGTRKI>SI

Parental  SYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRD
          .Y.G......V.FS.E..QARR.WN.IFK.LK.KNLQPRIL.PAKIFF..E.EIK.F.D..KLR.
Retrocopy TYRGKSVQMTVNFSSENKQARRKWN-IFKVLKEKNLQPRILHPAKIFFGDESEIKIFLDEGKLRE

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	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_142 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_142 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009821	7 retrocopies	retro_ecab_137, retro_ecab_142 , retro_ecab_237, retro_ecab_394, retro_ecab_643, retro_ecab_731, retro_ecab_925,