RetrogeneDB ID: retro_ecab_137

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:90823330..90824002(+)
• 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_137
GAGATGAAAAACACAATGGGTGAGATAAAGCAAGAATACAGATTCCCTGAACAATAGAGCTGAAACCATGGAGGAACGAA
TCACCAAAATTGAGGCTAGAAACAGAGACACACTTCAGATGGAGGAATAGAGAGAAGTAAGGCTAAAATGAAATGAAGAA
AGACTCCGAGAAATATCCGACTCGATTAGGAAATGCACTATAAGAACTATAGGTATTCCAGAGAGTGAAGAGAAGGAGAA
TGGAGCAGAAAGCTTCAATAGCAGAGAACTTCCCAAAACTGGGAAAGAGGATGGAAATCCATGTGGAAGAGGGTACCAGA
TCTCCTAAATACGTCAATGTATACAGACCTACTGAAAGGCATACAGCAGAGAAACTGGCAAAAGTGAATTAGAAATAAAA
AATACTAAGGGCAGCAATGCAGAAGAAAATACCTTACAAAGGAACCCCTATCGGGCTCTCAGTGGATTTCTCTGCAGAAA
CCTTTCAGGCTGGGAGAGACTGGAATGACATATTCAAATCCTTGAAGGAGAAAAACTTTCAGCCAAGGATACTTTATCCA
GTGAAAATATCCTTCAGATATGATGGAGAAATAAAAACTTTCCCAGATAAACAAAAGCTAAGGGAGTTCATAGCCACAAG
ACTACCCTGTGCAAGAAATCCTCAAGAAGGCC

Alignment

ORF - retro_ecab_137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.87 %
• Parental protein coverage: 92.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMKNTTLEMKS-SLERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRF
          EMKNT..E.K......LN.R.....E....I..R.....Q.E...E.R...NE..LRE..D.I....IR.
Retrocopy EMKNTMGEIKQ>NTDSLNNRAETMEERITKIEARNRDTLQMEE*REVRLK*NEERLREISDSIRKCTIRT

Parental  IGVPEGEERDKEAEN-RVAENFPNLKKETDIHIQEAQRTPKKISPKRATPRHIIIKISKMNDKERIPRAA
          IG.PE.EE....AE....AENFP.L.K...IH..E..R.PK.....R.T.RH...K..K.N.K..I.RAA
Retrocopy IGIPESEEKENGAES>SIAENFPKLGKRMEIHVEEGTRSPKYVNVYRPTERHTAEKLAKVN*K*KILRAA

Parental  RQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRD
          .QKKI.YKGTPI.LSV.FS.ET.QA.RDWNDIFK.LK.KN.QPRILYP.KI.FRY.GEIK.FPD.QKLR.
Retrocopy MQKKIPYKGTPIGLSVDFSAETFQAGRDWNDIFKSLKEKNFQPRILYPVKISFRYDGEIKTFPDKQKLRE

Parental  FVAT-SPPLQEILKKA
          F.AT...P.QEILKKA
Retrocopy FIAT>DYPVQEILKKA

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	0.03 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_137 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_137 has 0 orthologous retrocopies within eutheria group .

---

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,