RetrogeneDB ID: retro_ecab_884

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:58805687..58806224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSECAG00000016105
• Aliases: None
• Description: mitochondrial assembly of ribosomal large subunit 1 [Source:HGNC Symbol;Acc:21721]

Sequence

>retro_ecab_884
GACCGTGCTCGCGGCCTGCACGGGGGGCCCGGCCTGGAGGAGCTCGGGGAGCGGGCAGCCGGCGAGGGTCGCCCCGAGTC
AGGCACAGCAGATCATACTGGTCCCAAGTTTGACATCTATATGCTGGTTTCACTTCTGAGGCAAGAAAATGCAAGAGACA
TTTGTGTGATCAAGGTTCCTCCAGAAATGAAATACACAGATTAATTTGTGATTGGTAGTGGAACTTCCACGCGACGCTTA
CATGCCATGGCCTACTACATTGTGAAAATGTACAAATACCTGAAATGTAAAAGTGAGCCTCATGTTAAGATCGAAGGGAA
GGACACTGATGACTGGCTCTGTGTGGGCTTTGGCAGCATGGTGATTCATTTGATGCTTCCAGAAACCAGAGAAACCTATG
AATTAGAGAAATTATGGACCCTACGTTCTTACGATGACCAGTTAGCTCAGATAGCACCTGAGACATTACCTGAAGACTTC
ATTCTTGGAATAGAAGATGACACTTCATCCCTGACTCCAGTGGAGGTCAAATGTGAA

Alignment

ORF - retro_ecab_884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRARGLHGVTDLEELREQTAGEPRLESDTADHTGPKFDIDMLVSLLRQENARDICVIKVPPEMKYTDYFV
          DRARGLHG...LEEL.E..AGE.R.ES.TADHTGPKFDI.MLVSLLRQENARDICVIKVPPEMKYTD.FV
Retrocopy DRARGLHGGPGLEELGERAAGEGRPESGTADHTGPKFDIYMLVSLLRQENARDICVIKVPPEMKYTD*FV

Parental  IGSGTSTRHLHAMAYYIVKMYKYLKCKSEPHVKIEGKDTDDWLCVDFGNMVIHLMLPETRETYELEKLWT
          IGSGTSTR.LHAMAYYIVKMYKYLKCKSEPHVKIEGKDTDDWLCV.FG.MVIHLMLPETRETYELEKLWT
Retrocopy IGSGTSTRRLHAMAYYIVKMYKYLKCKSEPHVKIEGKDTDDWLCVGFGSMVIHLMLPETRETYELEKLWT

Parental  LRSYDDQLAQIAPETLPEDFILGIEDDTSSLTPVEVKCE
          LRSYDDQLAQIAPETLPEDFILGIEDDTSSLTPVEVKCE
Retrocopy LRSYDDQLAQIAPETLPEDFILGIEDDTSSLTPVEVKCE

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	1.77 RPM
SRP021940_cerebellum	0.00 RPM	2.96 RPM
SRP021940_embryo	2.07 RPM	2.81 RPM
SRP021940_placental_villous	2.93 RPM	2.89 RPM
SRP021940_synovial_membrane	2.80 RPM	2.28 RPM
SRP021940_testis	4.54 RPM	4.99 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_884 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884 ,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,