RetrogeneDB ID: retro_ecab_602

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:7754485..7755291(+)
• Located in intron of: ENSECAG00000009881

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012757
• Aliases: None
• Description: None

Sequence

>retro_ecab_602
AATGAAACAGAAATAAGCGACCAACCCAACAAAGAGTTCAAACAAAAACTCATAAGGATGCTCACAGATACTGGGAGAAG
ACTAGCTGAGCACAATGAGTTCATCAACAAAGAACTGGAAAATATAAAAAAGAATCAATCAGAAATGAAGACTACAATAC
TGGAACTGAAAAATTCACTAGAGGGACTCAATAGCAGAGTAGAGGATATAGAAGAACAGATCAGTGAGGTAGATGAAAGA
CTAGAGGAAATCACCCAAGCTGAATAGAAAAAAGATAATTAGACAGATTGAGAACAGTCTAAGGGAACTCTGGGACAATA
TCAAGCACACTAACATTCATATTATATGTGTCCCAGAAGGAGAAGAGAGAGACAAAAGGGCAGAAAATTTATTTGAAGAA
ATAATAGCTGAAAATTAACCTAACCTAAGGAAGGAAACAGATATCCAAGTACAGGAAGCACAGAGAGCTCCAAAAAAGAT
AAGCCCAAAGAGGCCCACACCAAGACACATTATAATTAAAATGTCCAAAATAAAAGAGAATCCAAAAAGTGGCAAGAGAA
AGGCAACAAGTGACAAACAAAGGAAAGCCCATAAGGCTATCAGCGGACTTCTCAGCCAAAACCCTACAGGCAAGAAGAGA
ATGGCATGATATACTTAAAATACTAAAAGGTAAAAACCTACAGCCAAGAATACTCTATCCATCAAGGTTGTCATTCAGAT
TGGCAGGAAAGATAAAGAGCTTCATAGACAAGCAAAAATTAAAGGAGTTTATCACCAAGAAACCAGTTCTACAAGAAATG
CTGAAG

Alignment

ORF - retro_ecab_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.12 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEKEINNVTDEEYKLTVIRVLTNLGRRMDELSENFKKELEN-KKRTNQKKTTILEIKNSLEGLNGRVDDT
          NE.EI......E.K...IR.LT..GRR..E..E...KELEN.KK.....KTTILE.KNSLEGLN.RV.D.
Retrocopy NETEISDQPNKEFKQKLIRMLTDTGRRLAEHNEFINKELENIKKNQSEMKTTILELKNSLEGLNSRVEDI

Parental  EEWISELDERLEEITQA-SQIKETRIIKNTNMVKELWDNIKHNNIRLVGVPEGAERDKGAENLFEEVIAE
          EE.ISE.DERLEEITQA....K..R.I.N.....ELWDNIKH.NI....VPEG.ERDK.AENLFEE.IAE
Retrocopy EEQISEVDERLEEITQA>NRKKIIRQIENS--LRELWDNIKHTNIHIICVPEGEERDKRAENLFEEIIAE

Parental  NFPNLRKETDWKTKKANRSPNFTNVKRPTPRHIVVKLAKVNDK-EKILRAARQNKITYKGTSIRLSENFS
          N.PNLRKETD.....A.R.P.....KRPTPRHI..K..K......K..R...Q...T.KG..IRLS..FS
Retrocopy N*PNLRKETDIQVQEAQRAPKKISPKRPTPRHIIIKMSKIKEN>QKVARERQQ--VTNKGKPIRLSADFS

Parental  ADTLQARREWNDIFRTLKDKNLQPRILYAVKISFKYDGEIKTFQDKQKLREFIATRPPLQEMLR
          A.TLQARREW.DI...LK.KNLQPRILY....SF...G.IK.F.DKQKL.EFI...P.LQEML.
Retrocopy AKTLQARREWHDILKILKGKNLQPRILYPSRLSFRLAGKIKSFIDKQKLKEFITKKPVLQEMLK

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	0.10 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_602 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_602 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012757	4 retrocopies	retro_ecab_1053, retro_ecab_387, retro_ecab_602 , retro_ecab_990,