RetrogeneDB ID: retro_ecab_643

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 25:8724171..8724803(+)
• 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_643
CAGGAACTCAATAGCAGAGTAGATGATATAGAAGAATGGATCAGTGAGCTAAGCGAAAGACTAGAAGAAATCACCCAAGC
TGAAGAGATAAAAGGAAAAAAAATTAGACAGAATGAGAACATTCTAAGGGAATTCTGGGACAATATCAAGTGCAATAACA
TTCATATTATAGGTGTCTGAGAAGGAGAAGAGAGAAACAAAGGGGTAGAAAATCTATTTGAAGAAACAGTGGCTGAAAAT
TTTCCTAACCTAAGGAAGGAAACAGACATCCAAGTACAGGAAGCACAGAGAGCTCTAAAAAAGATAAGCCCAAAGAGGCC
CACACCAAGACACATTATAATTAAACTCTCCAAAATTAAGGATAGAGAATCCTAAAAGTTACAAGAGAAAGGCAATAAGT
GACATACAAAGGAAATCCCATAAGGCTATCAGTGGACTTCTCAGCCAAAAACCTACAGGTGAGAAGAGAATGACATGACA
TATTTAAAGTGCTAAAAACAAAAAACCAACAGCCAAGAATACTCTATCAAGCAAGGGTGTCATTCAGAATGGAAGGAGAG
ATAAAGAGCTTCCCAGAGAAGCAAAAACTAAAGGAATTTATCACCAAGAAACTGGTTCTACAAAAAATGCTG

Alignment

ORF - retro_ecab_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 85.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERLNSRVSDTHEQMSEIDERLEEISQAEQKKEKRIRQNENSLRELWDNIKCTNIRFIGVPEGEERDKEAE
          ..LNSRV.D..E..SE..ERLEEI.QAE.......RQNEN.LRE.WDNIKC.NI..IGV.EGEER.K..E
Retrocopy QELNSRVDDIEEWISELSERLEEITQAEEXXXXXXRQNENILREFWDNIKCNNIHIIGV*EGEERNKGVE

Parental  N----RVAENFPNLKKETDIHIQEAQRTPKKISPKRATPRHIIIKISKMNDKERIPRAARQKK-ISYKGT
          N.....VAENFPNL.KETDI..QEAQR..KKISPKR.TPRHIIIK.SK..D.E.........K...YKG.
Retrocopy NLFEETVAENFPNLRKETDIQVQEAQRALKKISPKRPTPRHIIIKLSKIKDRES*KLQEKGNK<VTYKGN

Parental  PIRLSVHFSTETLQARRDWNDIFKTLKDKNLQPRILYPAKIFFRYEGEIKSFPDNQKLRDFVATSPPLQE
          PIRLSV.FS...LQ.RR...DIFK.LK.KN.QPRILY.A...FR.EGEIKSFP..QKL..F......LQ.
Retrocopy PIRLSVDFSAKNLQVRRE*HDIFKVLKTKNQQPRILYQARVSFRMEGEIKSFPEKQKLKEFITKKLVLQK

Parental  IL
          .L
Retrocopy ML

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	0.03 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_643 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_643 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,