RetrogeneDB ID: retro_ecab_695

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:43802872..43803224(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012904
• Aliases: None
• Description: None

Sequence

>retro_ecab_695
TTAGAAACCATAAAAAGTAGAGCTGAAGTTATGGAGGACAGAATTAGTGAATTAGAGGACAGAAATATAGAAATGCTTCA
GATAGCTGAGGAGAGAGAACTAAGATTTAAAAGATGAAGAAATTCTTTGAGAAATCTGACTCAATTAATGAAAGCAATAT
AAGGATTATAGGTATTCCAGAGGGGGAAGAGAGAGATAAAGGAGCATAGAGCTTGTTGAAAGAAATAACAGCTGAGAACT
TCCCAAACCTGGCGAAGAAACTGGACTTACAAATACATGAAGACAATACAACTCCTAATTACATCATGTAAACAGACTTT
CTCCAAGTCATATAATACTAAAACTGGCAAAA

Alignment

ORF - retro_ecab_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.02 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VESINNRMDQAEETC-ELEDRTFEIIQSEENKEKRMK-KIKDSLLEKYLTIRKSNIRIIGIPEGEEKQKD
          .E.I..R....E....ELEDR..E..Q..E..E.R.K.K.K....EK...I..SNIRIIGIPEGEE..K.
Retrocopy LETIKSRAEVMEDRISELEDRNIEMLQIAEERELRFK<KMK-KFFEKSDSINESNIRIIGIPEGEERDKG

Parental  TESLFKEIIAENFPNLGKKLDLQVHEANRTPNYI-KAKRPSPRHIVLKLVK
          ..SL.KEI.AENFPNL.KKLDLQ.HE.N.TPNYI....R.SP.HI.LKL.K
Retrocopy A*SLLKEITAENFPNLAKKLDLQIHEDNTTPNYI<HVNRLSPSHIILKLAK

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	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_695 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_695 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012904	11 retrocopies	retro_ecab_1003, retro_ecab_1068, retro_ecab_1117, retro_ecab_155, retro_ecab_407, retro_ecab_695 , retro_ecab_702, retro_ecab_768, retro_ecab_856, retro_ecab_877, retro_ecab_906,