RetrogeneDB ID: retro_ecab_394

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:28633062..28633727(+)
• 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_394
GAGAGAAAGAACACAATGAATGAGATTTTTTTTAAAAATCTAGAAACTTTAAAAAACAGAGCTGAAGTTATGGAGGACAG
ACTTAGTGATTTAGAGGACAGAAATATAGAAATGCAGGTGGAGAAGGAGCGAGAACTAAGACTTTTAAACAATGAAGAAG
TTCTTCAAGAAATATCCAACTCAATTAGGAAATGCAACATAAGGATTACAGGTATTCCAGAGAGAGAAAGGAGCAGAGAG
CTTGTTCAAAGAAATAATTAGAACTTCCCAAACCTGGGGAAAGAATTGGACTTACGAGTACATGAAGTCAATAGAACTCT
TAATTACATCAATGCAAAAGACCTTCTCCAAGGCATATAATAGTAAAACTGGCAAAAGTTAATGACAAAGAAAAAATATC
AAGAGCAGCAAGGCAGAAGAAAATAACCTACAAAGGAACCCTTATCAAACTTTCAACAGATTTCTTAGCAGAAACCTTAC
AGGCTAGGAGAGATTGGAATGATATATTCAAAATTCTGAAAGACAAAAACTTTCAGCAAAGAATACGCTATCCAGCAAAA
CTATCCTTCAGATACAATAGAGAAATAAAGGCTTTCCCAGTTTAACAAAAGTTGAGCGAGTTCATCACCACTAGACCTCC
CTTAAAAGAAATGAGGAAGGATGCC

Alignment

ORF - retro_ecab_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.44 %
• Parental protein coverage: 92.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMKNTTLEMK-SSLERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRF
          E.KNT..E.....LE.L..R........S....R..E..Q.E...E.R...NE..L.E....I...NIR.
Retrocopy ERKNTMNEXXXKNLETLKNRAEVMEDRLSDLEDRNIEM-QVEKERELRLLNNEEVLQEISNSIRKCNIRI

Parental  IGVPEGEERDKEAENRVAENFPNLKKETDIHIQEAQRTPKKISPK-RATPRHIIIKISKMNDKERIPRAA
          .G.PE..ER..E...R...NFPNL.KE.D....E..RT...I..K.R..PRHII.K..K.NDKE.I.RAA
Retrocopy TGIPE-RERSRELVQRNN*NFPNLGKELDLRVHEVNRTLNYINAK<RPSPRHIIVKLAKVNDKEKISRAA

Parental  RQKKISYKGTPIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRD
          RQKKI.YKGT.I.LS..F..ETLQARRDWNDIFK.LKDKN.Q.RI.YPAK..FRY..EIK.FP..QKL..
Retrocopy RQKKITYKGTLIKLSTDFLAETLQARRDWNDIFKILKDKNFQQRIRYPAKLSFRYNREIKAFPV*QKLSE

Parental  FVATSPPLQEILKKA
          F..T.PPL.E..K.A
Retrocopy FITTRPPLKEMRKDA

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_394 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_394 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,