RetrogeneDB ID: retro_ecab_629

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:32037077..32037375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR2
• Ensembl ID: ENSECAG00000009193
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 [Source:HGNC Symbol;Acc:29796]

Sequence

>retro_ecab_629
CTGACTAATGAGGGAACTCTGCTGCCCTGACCAGGTAACAGGATATAGATGCCCCGGTCACCACAGCCATCACCAGTAAC
ATCTGGGCCACCTAGAACCAGAACAGGAACCAAGCGTTGAATGAAGACAATCTCAAATTCATCCTCACGGACTGCACGAA
GGGCGGTGCAGCCATCACCTGGGTGGCCAGCCTTCTGCTGTGTATGCGTGCCAAGGAGACATGGGCTTCCGAATCTTCAA
GGCCAAGGCCCAGGCCTTGGAACAGTGGCTGGAGGAGCCTCTCGCCCAAGTAGTAGCA

Alignment

ORF - retro_ecab_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNNEGSLLAYSGYG-DTDARVTAAIASNIWAAYDRNGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCM
          L.NEG.LL...G...D.DA.VT.AI.SNIWA....N.NQA.NEDNLKFIL.DC..G..AIT.VA.LLLCM
Retrocopy LTNEGTLLP*PGNR<DIDAPVTTAITSNIWAT*NQNRNQALNEDNLKFILTDCTKGGAAITWVASLLLCM

Parental  YAKET-VGFGMLKAKAQALVQYLEEPLTQVAA
          .AKET..GF...KAKAQAL.Q.LEEPL.QV.A
Retrocopy RAKET<MGFRIFKAKAQALEQWLEEPLAQVVA

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	8.26 RPM
SRP021940_cerebellum	0.10 RPM	27.42 RPM
SRP021940_embryo	0.00 RPM	25.55 RPM
SRP021940_placental_villous	0.00 RPM	34.40 RPM
SRP021940_synovial_membrane	0.00 RPM	34.86 RPM
SRP021940_testis	0.00 RPM	33.19 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_629 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009193	1 retrocopy	retro_ecab_629 ,
Felis catus	ENSFCAG00000028596	1 retrocopy	retro_fcat_872,
Myotis lucifugus	ENSMLUG00000023871	1 retrocopy	retro_mluc_237,
Mus musculus	ENSMUSG00000028062	1 retrocopy	retro_mmus_878,
Otolemur garnettii	ENSOGAG00000016953	2 retrocopies	retro_ogar_2919, retro_ogar_910,
Pteropus vampyrus	ENSPVAG00000010328	1 retrocopy	retro_pvam_748,
Rattus norvegicus	ENSRNOG00000019908	3 retrocopies	retro_rnor_1037, retro_rnor_2493, retro_rnor_847,
Tursiops truncatus	ENSTTRG00000013344	1 retrocopy	retro_ttru_1782,