RetrogeneDB ID: retro_ecab_760

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 31:13985482..13986059(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUB1
• Ensembl ID: ENSECAG00000002621
• Aliases: None
• Description: OTU domain, ubiquitin aldehyde binding 1 [Source:HGNC Symbol;Acc:23077]

Sequence

>retro_ecab_760
TACTCACATACCTGCAAGACCAGGCCTGATGGGAACTGCTTCTATGGAGCTTTGGGATTCTGCCACTTGGAGGCGCTGCT
GAGTGACAGCAAGGAATTGCAGCCATCCAAGGCTGTGTCTTCCAAGAGCAAAGAGGACCTGGTGTCCCAGGGCTTCACTG
AGTTCACAACTGAGATATTTCATAACACGTTTGTGGACCTGATGGAACAGGGAGAGAAACAGACCTCAGTCGTCGACCTG
CTGACCTCTTTCAACAATCAGAGTACCTCAGACTTCTTGGAGGTCTACCTACGACTGCTCGCTTCAGGCTACCTGCAGCA
GGAGACCAAGTTCTTCCAGCACTTCATCGAGGGTGAGCGACTGTCAAGGAATTCTGCCAGCAGAAGGTGGAGCCCATGTG
CAAGGAGAGTGACCACATCCACGTCATCGCGCTGGCCGCGCCCCCAATGTCTCCATCCAGGTAGAATACATGGACCGCTG
TTAGGGCAGCACCAGCAAACTACAGATCTTCCCTGAGGGCTCTAAGCCCCAGGCCCACCTTCTCTACTGGCCTGAACACT
AGGATATCCTCTACAAA

Alignment

ORF - retro_ecab_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 75.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQ
          YS...KTRPDGNCFY.A.GF.HLEALL.DSKELQ..KAVS.KSKEDLVSQGFTEFT.E.FHNTF.DL.EQ
Retrocopy YSHTCKTRPDGNCFYGALGFCHLEALLSDSKELQPSKAVSSKSKEDLVSQGFTEFTTEIFHNTFVDLMEQ

Parental  VEKRTSVADLLASFNDQSTSDYLVVYLRLLTSGHLQRESTFFEHFIEGGR-TVKEFCQQEVEPMCKESDH
          .EK.TSV.DLL.SFN.QSTSD.L.VYLRLL.SG.LQ.E..FF.HFIEG.R.TVKEFCQQ.VEPMCKESDH
Retrocopy GEKQTSVVDLLTSFNNQSTSDFLEVYLRLLASGYLQQETKFFQHFIEGER<TVKEFCQQKVEPMCKESDH

Parental  IHIIALA-QALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK
          IH.IALA..A..VSIQVEYMDR..G.T....IFPEGS.P...LLY.P.H.DILYK
Retrocopy IHVIALA<RAPNVSIQVEYMDRC*GSTSKLQIFPEGSKPQAHLLYWPEH*DILYK

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	21.96 RPM
SRP021940_cerebellum	0.05 RPM	103.09 RPM
SRP021940_embryo	0.05 RPM	81.73 RPM
SRP021940_placental_villous	0.00 RPM	52.49 RPM
SRP021940_synovial_membrane	0.00 RPM	45.65 RPM
SRP021940_testis	0.00 RPM	202.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_760 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760 ,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131, retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87,