RetrogeneDB ID: retro_ecab_342

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:1177155..1177744(-)
• Located in intron of: ENSECAG00000008458

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000008327
• Aliases: None
• Description: None

Sequence

>retro_ecab_342
GAGCCATATGGCACATTAATCCTAAGTGGACCAGGTGGCTGCAGAAGCTGTGTAGTCCCTGCTGCTTTGGCTGTGATTGC
CTTGTCCTCAACCAGGGCTATCTCTCAGAGGCAGGGGCCAGCCTGGTGGACCAAAAACTGGAACTCAACATTGTGCCCCG
TACAAAGGTAGTATACCTGGCCAGTGAGACTTTCAACTATAGTGCCATTGACCGAGTGAAGTCCAAGGGCAAGCAGCTTG
CACTGGAGAAGGTGCCAAAACTTGGGCAGCAGTTTAACCACATTGGGCTACGGCTGAGGCCAAAGGTTAGTTCATTCCTG
CTCTTTGTTGAAGGCTACAAAGATGCAGATTACTGGCTACAGTGTTTTGAAGCAGAACCTCTCCCTGAGAACACTAACTG
GCAACTACTGCTTCAGTTTGAGCAGTTGTGGTACTGGATTACATCATCCGCAATACTGATCGAGGCAGTGACAACTGGCT
GATTAAATACCACTGTCCAATGGATAGTTCTAGCTCTCGGGACACAGACTGGGTGGTGGTGAAGGAGCCTGTTATCAAGG
TGGCTGCCATAGACAATGGGCTGGCTTTC

Alignment

ORF - retro_ecab_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.44 %
• Parental protein coverage: 54.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPYG-HLNPKWTKWLQKLCCPCCFGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA
          EPYG.H.NPKWT.WLQKLC.PCCFG.DCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA
Retrocopy EPYG<HINPKWTRWLQKLCSPCCFGCDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSA

Parental  IDRVKSRGKRLALEKVPKVGARFNRIG--LPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQ
          IDRVKS.GK.LALEKVPK.G..FN.IG..L.PKV.SF.LFVEGYKDADYWL..FEAEPLPENTN.QLLLQ
Retrocopy IDRVKSKGKQLALEKVPKLGQQFNHIGLRLRPKVSSFLLFVEGYKDADYWLQCFEAEPLPENTNWQLLLQ

Parental  FERL-VVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF
          FE.L.VVLDYIIRNTDRG.DNWLIKY.CPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF
Retrocopy FEQL<VVLDYIIRNTDRGSDNWLIKYHCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAF

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	0.06 RPM	10.21 RPM
SRP021940_cerebellum	0.05 RPM	19.47 RPM
SRP021940_embryo	0.08 RPM	12.40 RPM
SRP021940_placental_villous	0.10 RPM	24.54 RPM
SRP021940_synovial_membrane	0.03 RPM	16.44 RPM
SRP021940_testis	0.00 RPM	12.85 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_342 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_342 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008327	1 retrocopy	retro_ecab_342 ,