RetrogeneDB ID: retro_ecab_758

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 30:29753276..29753706(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERICH2
• Ensembl ID: ENSECAG00000011259
• Aliases: None
• Description: glutamate-rich 2 [Source:HGNC Symbol;Acc:44395]

Sequence

>retro_ecab_758
GGAGTTGGCAAAGATGCCGTCAATGCAGAGCAGGAGACAAATAACGAATATGGCTTTCAAGATATTGATGATAAGTTGTC
TGAATCAACAGATGATGGTGAAGATGATACCAATGATGAAGATTATGACAAAGACAGTAACCCTAATTAGGATCTTCACG
CACCATTAGAGTTAATGGCAAAATTCCTGGGAGCAGAACTGAGCCAAGACTACCATTTGACAAAAAAATTTATGTCAGAT
GATTCTAATCTATGAACCAGAAAATCCTGAGGCCAAGGAGTTTTTCTCACTTATTGAAGAAATGTTGCTGATGGAGAAAG
CTCAGAATCTTGAGGACGATGATGAAGATAGTGAAGAAAACAGGAGCGGTGGGAGTGAAGGGGAGAGCAGCGAGGGTCTG
AGTGAAGAAAGCTCCAACGAATGTGAGGAC

Alignment

ORF - retro_ecab_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.07 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVGKDAVIAEQEKISEYCLQDIDDKLSESTDDDGEDDTNDEDNDEDSTSNKDTHAPLELMAEFLRAEMSQ
          GVGKDAV.AEQE...EY..QDIDDKLSESTDD.GEDDTNDED.D.DS..N.D.HAPLELMA.FL.AE.SQ
Retrocopy GVGKDAVNAEQETNNEYGFQDIDDKLSESTDD-GEDDTNDEDYDKDSNPN*DLHAPLELMAKFLGAELSQ

Parental  DYHLAKK-LCQMILIYEPENPEAKEFFSLIEEMLLMEKTQTLEEDDEDSEEDSSGESEGESSEDLSEESS
          DYHL.KK.LCQMILIYEPENPEAKEFFSLIEEMLLMEK.Q.LE.DDEDSEE..SG.SEGESSE.LSEESS
Retrocopy DYHLTKK>LCQMILIYEPENPEAKEFFSLIEEMLLMEKAQNLEDDDEDSEENRSGGSEGESSEGLSEESS

Parental  DECED
          .ECED
Retrocopy NECED

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	1.06 RPM
SRP021940_cerebellum	0.00 RPM	0.36 RPM
SRP021940_embryo	0.00 RPM	1.15 RPM
SRP021940_placental_villous	0.00 RPM	0.24 RPM
SRP021940_synovial_membrane	0.00 RPM	0.33 RPM
SRP021940_testis	0.00 RPM	34.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_758 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011259	1 retrocopy	retro_ecab_758 ,
Myotis lucifugus	ENSMLUG00000010055	1 retrocopy	retro_mluc_2017,