RetrogeneDB ID: retro_ecab_883

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:47704123..47704481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSECAG00000012452
• Aliases: None
• Description: autophagy related 12 [Source:HGNC Symbol;Acc:588]

Sequence

>retro_ecab_883
ATGGCTGAGGAGCCAGCGTCCACGCTGCAGCTCCCTCCCTCAACTGCTGTGATGGCGAAGGACCTATGGAGGTCTCCCCA
GGAACAGCCACTCTGGAGCCCCCTTCTTCCCCTGCAGTCTCCCTCGGAACAAAGGAACCTGACACCAAGAAAAAAAGTGA
CATCCTGCTAAAGGCTGTGGGAGACACCCCTACCATGACGACAAAGCGGGATGTAGAGTGAACCCGAACCATCCACAGAC
TCATTGACTTCACCAAAAAGTTCCTTAAACTGTAGCCTCAGAACAGTTGTGTATCTATGTGAATCAGTCCTGTGCCCCGT
CCCCAGATGGGGAAGTTGGAACCCTCTATGAGTGTTTT

Alignment

ORF - retro_ecab_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 87.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEEPESALQLSPSTAA-DGEGPTEVSPETATPEPPSSAAVSPGTEEPAGDTKKKIDILLKAVGDTPIMK
          MAEEP.S.LQL.PSTA..DGEGP.EVSP.TAT.EPPSS.AVS.GT.EP..DTKKK.DILLKAVGDTP.M.
Retrocopy MAEEPASTLQLPPSTAV<DGEGPMEVSPGTATLEPPSSPAVSLGTKEP--DTKKKSDILLKAVGDTPTMT

Parental  TKKWAVERTRTIQGLIDFIKKFLKL-VASEQLFIYVNQSFAPSPDQEVGTLYECF
          TK...VE.TRTI..LIDF.KKFLKL.VASEQL.IYVNQS.APSPD.EVGTLYECF
Retrocopy TKR-DVE*TRTIHRLIDFTKKFLKL<VASEQLCIYVNQSCAPSPDGEVGTLYECF

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	7.79 RPM
SRP021940_cerebellum	0.00 RPM	12.31 RPM
SRP021940_embryo	0.03 RPM	12.61 RPM
SRP021940_placental_villous	0.00 RPM	7.65 RPM
SRP021940_synovial_membrane	0.00 RPM	6.84 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_883 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883 ,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,