RetrogeneDB ID: | retro_ecab_1079 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:69842614..69843400(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SH3GLB2 | ||
| Ensembl ID: | ENSECAG00000004437 | ||
| Aliases: | None | ||
| Description: | SH3-domain GRB2-like endophilin B2 [Source:HGNC Symbol;Acc:10834] |
Retrocopy-Parental alignment summary:
>retro_ecab_1079
GTGCCACTGTGGCCCAACCCCAGTGCCCGAGTGGAGGAGTTTCCATATGAGAAGCTAGACAGGAAGCTGACTTTGTGGGT
CACCAATATGGAACTGCTGCATCAGTCCATGTCAGAGATGGCCAGTGGGCTGGGCCCCACTGCTACCTAGGGGAAGACAT
TGATCAAGGTGGCAGAAACTGAAAAGTGCCTGGGAGATACAGAAGATTTTATCCTCATAGCCCCCACCAACTTCCTCATG
TCCCAGTGCAACTTCCAAGAAGGGGGCTGGAAGATGATTTCCAAGGAGGGGTGGCTCCTCCAAAACCTGTGTCTGGACTT
GAATGCCTGCAAAGCACTCCTGAAGAAGGCCAAGGCTGCAGAAGCCAAAGCCACAATGGTGCTTGAATTTCAGGAGACTT
GACCTTGTAATTAAATTCTCTCCAGCAGCGCCTCCCTGCTTTGGAATGATGAGGTGGACAAGACTGAGCAGGAGCTCCAA
GTAGCCCCAAAGGAGGTCGACCAGCAGGCAGAAGTGACCAGTCTCCTGCTGGAGGGAATCAGCTGCATTCACATGAAGCA
TCTTCGTTGCCTCTGTGAGTTCCTAGAGTCTCAGACAACTTATTACGTGCAGTGCTACTGCTGCATGCTGGACTTACATA
AACAGCTGGACAGATTTCCAGGCACCTTCATGGGTACAACAGAACCCACCTACCTGCCCCTGAGCAGCAAGTCACCCACC
ACCACAGCTACTGTGCCTGTGGTACCCTCTGTGGCTGGCCTGGCCTCTTTGGGGGAACCTGCTCTG
ORF - retro_ecab_1079 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.21 % |
| Parental protein coverage: | 70.4 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLLQPNPSARVEEFLYEKLDRKVPSRVTNGELLAQYMAEAASELGPTTPYGKTLVKVAEAEKRLGAAERD |
| V.L.PNPSARVEEF.YEKLDRK....VTN.ELL.Q.M.E.AS.LGPT...GKTL.KVAE.EK.LG..E.D | |
| Retrocopy | VPLWPNPSARVEEFPYEKLDRKLTLWVTNMELLHQSMSEMASGLGPTAT*GKTLIKVAETEKCLGDTE-D |
| Parental | FIHTASINFLTPLRNFLEGDWKTISKERRLLQNRRLDLDACKARLKKAKAAEAKATTVPDFQETRPRNYI |
| FI..A..NFL....NF.EG.WK.ISKE..LLQN..LDL.ACKA.LKKAKAAEAKAT.V..FQET.P.N.I | |
| Retrocopy | FILIAPTNFLMSQCNFQEGGWKMISKEGWLLQNLCLDLNACKALLKKAKAAEAKATMVLEFQET*PCN*I |
| Parental | LSASASALWNDEVDKAEQELRVAQTEFDRQAEVTRLLLEGISSTHVNHLRCLHEFVESQTTYYAQCYRHM |
| LS.SAS.LWNDEVDK.EQEL.VA..E.D.QAEVT.LLLEGIS..H..HLRCL.EF.ESQTTYY.QCY..M | |
| Retrocopy | LSSSASLLWNDEVDKTEQELQVAPKEVDQQAEVTSLLLEGISCIHMKHLRCLCEFLESQTTYYVQCYCCM |
| Parental | LDLQKQLGRFPGTFVGTTEPTSPPLSSTSPTTTAATMPVGPSVAGLGPPGEAAL |
| LDL.KQL.RFPGTF.GTTEPT..PLSS.SPTTT.AT.PV.PSVAGL...GE.AL | |
| Retrocopy | LDLHKQLDRFPGTFMGTTEPTYLPLSSKSPTTT-ATVPVVPSVAGLASLGEPAL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 | 20 .90 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 254 .99 RPM |
| SRP021940_embryo | 0 .00 RPM | 48 .56 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 78 .04 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 32 .04 RPM |
| SRP021940_testis | 0 .00 RPM | 11 .25 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1079 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1079 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1079 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020282 | 1 retrocopy | |
| Equus caballus | ENSECAG00000004437 | 1 retrocopy |
retro_ecab_1079 ,
|