RetrogeneDB ID: retro_ecab_280

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:20550217..20550622(+)
• Located in intron of: ENSECAG00000020012

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSECAG00000023306
• Aliases: None
• Description: RAB5B, member RAS oncogene family [Source:HGNC Symbol;Acc:9784]

Sequence

>retro_ecab_280
CAGTGGAGAAGTCTAGCTTGGTATTACGATTTGTCAAAAGGCAGTTCCATGAGTACCAAGAGAGCACCATTGGAGGAAAC
CTTTGCTCGAGCAAAGACATGGGTAAAGGTACTACAGCGACAGGCTAGTCTTAGCATCATTATTGCCCTGGCAGGGAACA
AAGCTGACCTGGCCAACAAGCGCATGGTGGAGTATGAAGAGGCCCAGGTGTATGCAGATGACAACAGCTTATTGTTTATG
GAGACCTCAGCCAAGACAGCTACGAACGTGAATGACCTCTTCCTGGCAATAGGTAAGAAGTTGCCAAAGAGTGAACCCCA
GAATCCAGGGGGTGCAGCAGGCCGAAGCCAGGGTGTGGATCTCCATGAGCACTCCCAGCAGAACAAGAGCCAGTGTTGTA
GCAAC

Alignment

ORF - retro_ecab_280 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 62.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQA
          ...SLA..Y................ETFARAKTWVK.LQRQAS.SI.IALAGNKADLANKRMVEYEEAQ.
Retrocopy QWRSLAWYYDLSKGSSMSTKRAPLEETFARAKTWVKVLQRQASLSIIIALAGNKADLANKRMVEYEEAQV

Parental  YADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNPGGAAGRSRGVDLHEQSQQNKSQCCSN
          YADDNSLLFMETSAKTA.NVNDLFLAI.KKLPKSEPQNPGGAAGRS.GVDLHE.SQQNKSQCCSN
Retrocopy YADDNSLLFMETSAKTATNVNDLFLAIGKKLPKSEPQNPGGAAGRSQGVDLHEHSQQNKSQCCSN

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	0.12 RPM	1.71 RPM
SRP021940_cerebellum	0.10 RPM	3.53 RPM
SRP021940_embryo	0.13 RPM	96.97 RPM
SRP021940_placental_villous	0.10 RPM	89.68 RPM
SRP021940_synovial_membrane	0.11 RPM	77.17 RPM
SRP021940_testis	0.13 RPM	83.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_280 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_280 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280 ,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,