RetrogeneDB ID: retro_ecab_192

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:141084877..141085563(-)
• Located in intron of: ENSECAG00000026853

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000005242
• Aliases: None
• Description: None

Sequence

>retro_ecab_192
AACACAGACAGAACTTCAACAAAGACAGAAAATATAAAAAAAGTACCAAACAGAAGTCACAGAGCTGAAGAATACAATAA
CTAAACTGAAAAATACACTACAGGGGTTCAACAGTAGGCTAGATGAAGTAGAAGAAAGGATCAGTGACCTGGAAGACAGT
ACCGTGGAACTTACCCAAACAGAACAGCAAAAAGAAAAAAGAATTTTAAAAAGCAAAGATAGCTTAAGAGACCTACGGGA
CGAGATCAAGCAGAACAACATTCACGTTATAGGGGTCCAAGAGAGAGAAAGGGACAGAAAATTCATTTGAGGAAATAATA
GCTGAAAACTTCCCTATTGAGGGAAGGAGACAGACATCCAGATCTGGGAAGTGCAGAGAGTTCCAAATAAGATGAACCCA
AAAAGATCCACACAAAGACACATTATAATTAAAATGTGAACTTAGATAAAGAGGAAATCTTAAAAGCAGCAAGAAAAAAA
CAATTTGTTACATACAAGGGAACCTCCATAAGACTATCAGCAGGTTTTCCAGCAGAAATTTGGCAGGCCAGAAGAGAGGG
GCATGATATATTCAAAGTGCTGAAAGCAAAAACCTGCCCACCAAGAATACTCTACCCAGCAAGGTTATCAATCAGAATTG
AAGGAGAGATAAAGAGTTTTCCAGCCAAGAAAAGCTAAAGGAGTTC

Alignment

ORF - retro_ecab_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.21 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HSENFSKETENIRK-YQIEVTELKNTPTELKNTIEGFKSRLDDTEERISGLEDRAVELIQSELSTQNRLE
          .....S..TENI.K.YQ.EVTELKNT.T.LKNT..GF.SRLD..EERIS.LED..VEL.Q.E........
Retrocopy NTDRTSTKTENIKK>YQTEVTELKNTITKLKNTLQGFNSRLDEVEERISDLEDSTVELTQTEQXXXXXXX

Parental  DLAPSPKDCADSMRKCSIRTIGVQEGEE-KEDGAESVLKEIIAENFPNLG-DEREMCVEEVFRSPRYVNV
          ....S..D..D......I..IGVQE.E...E...E....E....NFP..G..E......EV.R.P...N.
Retrocopy XXXXSLRDLRDEIKQNNIHVIGVQERER>TENSFEEIIAE----NFPIEG<KETDIQIWEVQRVPNKMNP

Parental  KRPTARHIVVKL-AKMNDKERILRAARLKK-ITYKGTPIRLSVDFSAETLQARTDWNDIFKTLKDKNLQP
          KR.T.RHI..K........E.IL.AAR.K...TYKGT.IRLS..F.AE..QAR....DIFK.LK.K...P
Retrocopy KRSTQRHIIIKM<VNLDKEE-ILKAARKKQFVTYKGTSIRLSAGFPAEIWQARREGHDIFKVLKAKTCPP

Parental  RILYPAKISFRYEGEIKSFPEK-QKLRDF
          RILYPA..S.R.EGEIKSFP.K..KL..F
Retrocopy RILYPARLSIRIEGEIKSFPAK<EKLKEF

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	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.03 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_192 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_192 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005242	2 retrocopies	retro_ecab_192 , retro_ecab_934,
Equus caballus	ENSECAG00000006639	4 retrocopies	retro_ecab_274, retro_ecab_484, retro_ecab_671, retro_ecab_689,