RetrogeneDB ID: | retro_ecab_288 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 13:19674539..19675297(-) | ||
| Located in intron of: | ENSECAG00000014460 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CAB39 | ||
| Ensembl ID: | ENSECAG00000015288 | ||
| Aliases: | None | ||
| Description: | calcium binding protein 39 [Source:HGNC Symbol;Acc:20292] |
Retrocopy-Parental alignment summary:
>retro_ecab_288
TTGAAGGAAATTCCGTATGGTACAAATGAAAAAGAACCACAGACAGAAGCGGCGGCCAACTCGCTCAAGAACTCTGTAAC
AGTGGGCTCCTTAGCACCCTGGTAGCTGACTTACAGCTCATTGACTTTGAGGGCAAAAAAAGATGTGGCTCAAATTTTCA
ACAATATTCTCAGAAGACAAATTGGTACAAGAACTCCCACTGTTGAATACATCTGCACCCAACAGAATATTTTGTTCGTG
TTATTGAAAGGGTATGAATCTCCAGAAATAGCTCTAAATTGTGGAATAATGTTGAGAGAATGCATCAGACACGAACCACT
TGCAAAAATCATTTTTGGTCAGAACAATTTTATGATTTCTTCAGATGTGTCGAAATGTCAATATTTGACGTAGCTTCAGA
TGCATTCGCCACATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAACAGCATTATGATAGAT
TCTTCAGTGAACATGAGAAGTTACTTCATTCAGAAAATTAGGTGACAAAAAGACAGTCACCCAAGCTTCTCGGTGAGTTA
CTATTAGACAGACACAACTTCACGATTATGACAAAATCCATCAGTAAACCTGAGAACCTCAAATTAATGATGAACCTTCT
GCGAGACAAAAGTTGTAACATCCAATTTGAGGCCTTTCACATTTTTAAGGTGTTTGTAGCCAATCCTAACAAGACACAGC
CCATCCTCAACATCCTCCTCTAGAACCAGACCAAACTC
ORF - retro_ecab_288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.19 % |
| Parental protein coverage: | 74.19 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MKEILYGTNEKEPQTEAVA-QLAQELYNSGLLSTLVADLQLIDFEGKK-DVAQIFNNILRRQIGTRTPTV |
| .KEI.YGTNEKEPQTEA.A.QLAQEL.NSGLLSTLVADLQLIDFEGKK.DVAQIFNNILRRQIGTRTPTV | |
| Retrocopy | LKEIPYGTNEKEPQTEAAA<QLAQELCNSGLLSTLVADLQLIDFEGKK>DVAQIFNNILRRQIGTRTPTV |
| Parental | EYICTQQNILFMLLKGYESPEIALNCGIMLRECIRHEPLAKIIL-WSEQFYDFFRYVEMSTFDIASDAFA |
| EYICTQQNILF.LLKGYESPEIALNCGIMLRECIRHEPLAKII..WSEQFYDFFR.VEMS.FD.ASDAFA | |
| Retrocopy | EYICTQQNILFVLLKGYESPEIALNCGIMLRECIRHEPLAKIIF<WSEQFYDFFRCVEMSIFDVASDAFA |
| Parental | TFKDLLTRHKLLSAEFLEQHYDRFFSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENL |
| TFKDLLTRHKLLSAEFLEQHYDRFFSE.EKLLHSEN.VTKRQS.KLLGELLLDRHNFTIMTK.ISKPENL | |
| Retrocopy | TFKDLLTRHKLLSAEFLEQHYDRFFSEHEKLLHSEN*VTKRQSPKLLGELLLDRHNFTIMTKSISKPENL |
| Parental | KLMMNLLRDKSRNIQFEAFHVFKVFVANPNKTQPILDILLKNQTKL |
| KLMMNLLRDKS.NIQFEAFH.FKVFVANPNKTQPIL.ILL.NQTKL | |
| Retrocopy | KLMMNLLRDKSCNIQFEAFHIFKVFVANPNKTQPILNILL*NQTKL |
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 | 13 .40 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 18 .44 RPM |
| SRP021940_embryo | 0 .00 RPM | 14 .19 RPM |
| SRP021940_placental_villous | 0 .10 RPM | 25 .93 RPM |
| SRP021940_synovial_membrane | 0 .08 RPM | 11 .31 RPM |
| SRP021940_testis | 0 .06 RPM | 27 .24 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_288 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_288 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_288 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013349 | 1 retrocopy | |
| Equus caballus | ENSECAG00000015288 | 1 retrocopy |
retro_ecab_288 ,
|
| Otolemur garnettii | ENSOGAG00000002000 | 1 retrocopy |