RetrogeneDB ID: | retro_ecab_627 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 24:3540427..3541533(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HERPUD1 | ||
| Ensembl ID: | ENSECAG00000011366 | ||
| Aliases: | None | ||
| Description: | homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 [Source:HGNC Symbol;Acc:13744] |
Retrocopy-Parental alignment summary:
>retro_ecab_627
CTGGAGCTGAGCGGCGACCGCAGCTGGAGCGTGGCCGTCTCAAGGCTCCTCTGAGCCGCGTCTACCCCGAGCGCCCGCGG
CCAGAGGACCAGAGGTTAATTTATTCTGGGGAGCCGTTGTTGGATCACCGGTGTCTTAGGGACTTGCTTCCAAAGCAGGA
GAAACGGCACGTTTCGCATCTGGTATGCAATGTGAAGAGTCCTTCCAAAATGCCAGAAACCACCGCGAAGGTTGCTGAAG
CCACAGAGCAGCCTACTGGTCTTAATCAGGGACAGTATTCTGGGGATTCGCCAAGTGATGGTTTAAGGCAAAGGGAGGCT
CTCCGGAACCTTTCTCCCTCTGGATAGGAGAACATCTCCAGACCTGAAGCTGCCCAGCCGGCGTTCCAAGGCCGGGGGCC
TGGTTTCTCGGGCTACACAACCTATGGGTGGCTGCAGCTCTCCTGGTTCTAGCAGACGGACGCACGGCAGTACTGCATGC
AGTATTCAGCGGCCACTGCTGCATCAGGGGCTTCTGTGCCCTCACCAAGTGCACAAGAGATACCTGTGGTCTCCGCTCCT
GCTCCAGCAGCTCCCATTCACAACCAGTTTCCAGCGGAAAACCAGCCGGCCAATCAGAATGCTGCCCCTCAAGTGGGTGG
TTAATGCTGGGGCCAATCAGAATTTGCGGATGACCGCACAAGGTGGCCCTATTGTGGAAGATGATGATGAGATCAACCGA
GATTGGTTGGATTGGACCTATTCAGCAGCTATGTTTTCGGTTTTTCTCAGTATCCTCTAATTCTACTCCTCTCTCAGCAG
ATTCCTCATGGTCATGGGAGCCACCGTGGTTACGTACCTGCATCACGTTGGACGGTTTCCATTTAGACAGAGGCCAGTTC
AGAACTTCCCGAAGGATGGGCCCCCTTATGAAGCTGTGAATCAGGACCCCTACAATAACTTACAGGAACGCCCTGACCCT
GAAATCGAAGATCCCAACCACGTTCCTCCAGACAAGGACGTTCTGGATGGCGTGCAGACCAGCCCTTCATTTTATGAGCA
CAACCTGGCTTGTTTTCAAGACTCTTTGCCTCTCTTCTTCCAGAAGGGCCCCCAGCTATAGCAAAC
ORF - retro_ecab_627 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.03 % |
| Parental protein coverage: | 98.4 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | LELSGDRS-SV-GRLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPA |
| LELSGDRS.SV.GRLKA.LSRVYPERPRPEDQRLIYSG..LLDH.CLRDLLPKQEKRHV.HLVCNVKSP. | |
| Retrocopy | LELSGDRSWSV<GRLKAPLSRVYPERPRPEDQRLIYSGEPLLDHRCLRDLLPKQEKRHVSHLVCNVKSPS |
| Parental | KMPETSAKVAEAPEQPAGLNQGQYPGDSPGDGLRPREPLRNLSPSGWENISRPEAAQPAFQGLGPGFSGL |
| KMPET.AKVAEA.EQP.GLNQGQY.GDSP.DGLR.RE.LRNLSPSG.ENISRPEAAQPAFQG.GPGFSG. | |
| Retrocopy | KMPETTAKVAEATEQPTGLNQGQYSGDSPSDGLRQREALRNLSPSG*ENISRPEAAQPAFQGRGPGFSGY |
| Parental | TTYGWLQLSWLQQVYARQYYMQYLAATAASGAFVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA |
| TTYGWLQLSW..Q..ARQY.MQY.AATAASGA.VPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA | |
| Retrocopy | TTYGWLQLSWF*QTDARQYCMQYSAATAASGASVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA |
| Parental | PQV-VVNPGANQNLRMNAQGGPVVEEDDELNRDWLDWTYSAATFSVFLSILYFYSSLSRFLMVMGATVVM |
| PQV.VVN.GANQNLRM.AQGGP.VE.DDE.NRDWLDWTYSAA.FSVFLSIL.FYSSLSRFLMVMGATVV. | |
| Retrocopy | PQV>VVNAGANQNLRMTAQGGPIVEDDDEINRDWLDWTYSAAMFSVFLSIL*FYSSLSRFLMVMGATVVT |
| Parental | YLHHVGWFPFRQRPVQNFPNGGPPYDAVNQDPNNNLQEGPDPEIEDPSHGPPDRDALDGEQTSPS-FMST |
| YLHHVG.FPFRQRPVQNFP..GPPY.AVNQDP.NNLQE.PDPEIEDP.H.PPD.D.LDG.QTSPS.FMST | |
| Retrocopy | YLHHVGRFPFRQRPVQNFPKDGPPYEAVNQDPYNNLQERPDPEIEDPNHVPPDKDVLDGVQTSPS>FMST |
| Parental | AWLVFKTFFAS-LLPEGP-PAIAN |
| .WLVFKT...S.....GP.PAIAN | |
| Retrocopy | TWLVFKTLCLS<FFQKGP<PAIAN |
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 .18 RPM | 49 .88 RPM |
| SRP021940_cerebellum | 0 .47 RPM | 50 .95 RPM |
| SRP021940_embryo | 0 .18 RPM | 23 .65 RPM |
| SRP021940_placental_villous | 0 .43 RPM | 50 .18 RPM |
| SRP021940_synovial_membrane | 0 .14 RPM | 33 .38 RPM |
| SRP021940_testis | 0 .32 RPM | 43 .23 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_627 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_627 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_627 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000011366 | 1 retrocopy |
retro_ecab_627 ,
|