RetrogeneDB ID:

retro_ecab_350

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:15:66575435..66575803(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2I
Ensembl ID:ENSECAG00000015831
Aliases:None
Description:ubiquitin-conjugating enzyme E2I [Source:HGNC Symbol;Acc:12485]


Retrocopy-Parental alignment summary:






>retro_ecab_350
TTTGGTTTTGTGGCAGCGTCTACAGAAATTCTAGATGGCAGGATCAGTCTCATGAACTGGAAGAGTACCATTCCAGGAAA
GAGAGAAAAGAAAGAAACCCCATTGAAAAGAGACTTGTTTCAACTATGATTGTTTTTCAAGGAAGATTTTCCATTCTCAC
CACCATAATGAAAATTTAAACCACCATTACTTCACACAATGACTATCCTTCAAGAATAATGTGTCTGCCCATCTTAGAGG
AAGATAAGGATTAAAGTCCAGCAATTACAATTAAACATACCTTATTAGAAATACAGAAATTCCTAAATGAACCAAATATT
CAAAATCAACATTGCACAGGTTTGAGAATTTACTGCCAAAACAATATT

ORF - retro_ecab_350 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56. %
Parental protein coverage: 76.58 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFGFVAVPTKNPDGTMNLMNWECAIPG---KKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHP-NVY
FGFVA..T...DG...LMNW...IPG...KK.TP....LF.L...FK.D.P.SPP..KF.PPL.H..N.Y
RetrocopyFGFVAASTEILDGRISLMNWKSTIPGKREKKETPLKRDLFQL*LFFKEDFPFSPP**KFKPPLLHT<NDY
ParentalPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRV
PS...CL.ILEEDKD..PAITIK..LL.IQ..LNEPNIQ.........IYCQN..
RetrocopyPSRIMCLPILEEDKD*SPAITIKHTLLEIQKFLNEPNIQN-QHCTGLRIYCQNNI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP021940_articular_cartilage 0 .00 RPM 30 .58 RPM
SRP021940_cerebellum 0 .00 RPM 46 .43 RPM
SRP021940_embryo 0 .00 RPM 81 .81 RPM
SRP021940_placental_villous 0 .00 RPM 37 .82 RPM
SRP021940_synovial_membrane 0 .00 RPM 41 .84 RPM
SRP021940_testis 0 .00 RPM 37 .92 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_350 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_350 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_350 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000077211 retrocopy
retro_amel_1843,
Bos taurus ENSBTAG000000388661 retrocopy
retro_btau_1470,
Canis familiaris ENSCAFG000000314494 retrocopies
retro_cfam_1363, retro_cfam_1991, retro_cfam_2090, retro_cfam_541,
Callithrix jacchus ENSCJAG000000132491 retrocopy
retro_cjac_2914,
Cavia porcellus ENSCPOG000000104311 retrocopy
retro_cpor_156,
Equus caballus ENSECAG00000015831 1 retrocopy
retro_ecab_350 ,
Felis catus ENSFCAG000000272912 retrocopies
retro_fcat_1994, retro_fcat_873,
Loxodonta africana ENSLAFG000000183181 retrocopy
retro_lafr_541,
Myotis lucifugus ENSMLUG000000082292 retrocopies
retro_mluc_1112, retro_mluc_1327,
Macaca mulatta ENSMMUG000000036541 retrocopy
retro_mmul_981,
Mustela putorius furoENSMPUG000000157631 retrocopy
retro_mputfur_1234,
Mus musculus ENSMUSG000000151204 retrocopies
retro_mmus_1341, retro_mmus_1997, retro_mmus_3182, retro_mmus_3419,
Nomascus leucogenys ENSNLEG000000085251 retrocopy
retro_nleu_1298,
Otolemur garnettii ENSOGAG000000014284 retrocopies
retro_ogar_2367, retro_ogar_2731, retro_ogar_548, retro_ogar_641,
Rattus norvegicus ENSRNOG0000001790711 retrocopies
retro_rnor_1051, retro_rnor_1448, retro_rnor_1764, retro_rnor_1913, retro_rnor_2036, retro_rnor_2147, retro_rnor_2301, retro_rnor_2423, retro_rnor_2927, retro_rnor_708, retro_rnor_832,
Sarcophilus harrisii ENSSHAG000000070341 retrocopy
retro_shar_218,
Sus scrofa ENSSSCG000000215601 retrocopy
retro_sscr_319,
Ictidomys tridecemlineatus ENSSTOG000000102333 retrocopies
retro_itri_1341, retro_itri_1459, retro_itri_1601,




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