RetrogeneDB ID: retro_ecab_452

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:63507499..63507965(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNAU1AP
• Ensembl ID: ENSECAG00000012980
• Aliases: None
• Description: tRNA selenocysteine 1 associated protein 1 [Source:HGNC Symbol;Acc:30813]

Sequence

>retro_ecab_452
ATGGAGGCCCGCCTACGGATAGGTGCCCTGGAGCCTACGTGGATGAGAACTTCACTGCCAGAGCCCTTGCCTCCACAGGG
GAGACCAGGATAAGTGTCAAAATTACCCAAAACAGCCTCACTGGACTCCCAGCTGGCTGCTGTTTTGTAGAATGCACAGA
TTTGGCAACAGCTGGGAAGTGTTTGCATAAAATTAATGGGAAACATCATCTAAGAGCCACACCTGCAAAATGTTTTAAAG
TGAACTATGCCACTTGTAGGAAATAACCAAATAATAGCCCTGAGTACTGCCTCTTTTGGGGGAGGGTCTGATCCAAGATG
TGGATGATGGCAAGCTTTTAGAATTCTTCATCTACATCTGCCGCTCCTGTCAGGAAAGCAAGGTGGTTTTGGATGAGGGC
TATGGTTTTGTGAAACCATTGGGCTATGGTTTTGTCAAATTCACGGATGAATTCACAGATGAAAAG

Alignment

ORF - retro_ecab_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.13 %
• Parental protein coverage: 52.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASLWMGDLEP-YMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP
          M.A.L..G.LEP.Y.DENF..RA.A..GET..SVKI..N.LTG.PAG.CFVE..DLATA.KCLHKINGK.
Retrocopy MEARLRIGALEP<YVDENFTARALASTGETRISVKITQNSLTGLPAGCCFVECTDLATAGKCLHKINGKH

Parental  LPGATPAKRFKLNYATYGKQPDNSPEYSLF-VGD-LTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVS
          ...ATPAK.FK.NYAT..K.P.NSPEY.LF..G..L..DVDDG.L.EFF.....SC...KVVLD...G..
Retrocopy HLRATPAKCFKVNYATCRK*PNNSPEYCLF<LGEGLIQDVDDGKLLEFFIYICRSCQESKVVLDEGYGFV

Parental  KGYG--FVKFTDELEQKR
          K..G..FVKFTDE.....
Retrocopy KPLGYGFVKFTDEFTDEK

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	6.02 RPM
SRP021940_cerebellum	0.00 RPM	15.22 RPM
SRP021940_embryo	0.00 RPM	18.97 RPM
SRP021940_placental_villous	0.00 RPM	8.56 RPM
SRP021940_synovial_membrane	0.00 RPM	10.73 RPM
SRP021940_testis	0.00 RPM	23.47 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_452 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011367	1 retrocopy	retro_amel_1782,
Callithrix jacchus	ENSCJAG00000009717	1 retrocopy	retro_cjac_3928,
Equus caballus	ENSECAG00000008229	2 retrocopies	retro_ecab_684, retro_ecab_792,
Equus caballus	ENSECAG00000012980	1 retrocopy	retro_ecab_452 ,
Mustela putorius furo	ENSMPUG00000015511	2 retrocopies	retro_mputfur_1185, retro_mputfur_856,
Pelodiscus sinensis	ENSPSIG00000006864	1 retrocopy	retro_psin_41,
Tupaia belangeri	ENSTBEG00000008049	1 retrocopy	retro_tbel_923,