RetrogeneDB ID: | retro_ogar_2706 | ||
Retrocopy location | Organism: | Bushbaby (Otolemur garnettii) | |
| Coordinates: | GL873651.1:1878292..1879143(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HBP1 | ||
| Ensembl ID: | ENSOGAG00000013102 | ||
| Aliases: | None | ||
| Description: | HMG-box transcription factor 1 [Source:HGNC Symbol;Acc:23200] |
Retrocopy-Parental alignment summary:
>retro_ogar_2706
ATGGAGACTGATGAACTTTTGGAACTTCAGGCTGTTTAAAGTGGTCTTACCCAGTCTGCCATGTACCAGCTAAGTTGAGA
CATTTCAGATCAAGAATATTTAAGACCATCTTAAAACCCAAAATATCTCAGACATACCAGAAAATACTGGCTGTGAAACT
GAGGTAGTCTGGCTAACAGAATTAGTAAATATTACCACTAGTCCACAAAGTTCGCTTATGCAGTGCTCATTCTACAACAC
ATCATCATCTCCTGTACACATAAGAGCTACTAGCAAGTTCACATTCTTGTATGCCCCTCCACCCGGGTCCTCTTCTCCAA
GAGTGAGCCAGCCTTCCCTCATCACCACTGGAAGGAGGAAACACCAGTGAGGCATGAAAAGGCAAACATAACAAGTCAGA
ATCTAGTGTTCTCCACATGTCCACCCTGTCAGATAATGATGATCTGAGATGGTGCAATTCCTGGCCTTCAACTGTTTGGC
ACTATTTTTTGAAAGGCACAAAATTATACTTTCATGAGGGAAGCAATAAGGAACGGCGAGATGCTGAAGATTTTGCTAGA
GCTGAAAGCTGTGATGAGGAGGAAGGCCTTCAAATGAGCACTCAAAACAAGGGCTATAGCTGTGATGGTCTAAAGTTGTT
ATCACATGAAGAAAGTACATCATTTGCTGAGTCAGTACTGAAGTTGACTTTTGATCCTGGTACAGCAGAAGATGGTGTAC
TTACCATGGTATGTAGGCTGGACCACCCTTTCTATGTTAAAAATAAAGGCTAGTCATCGTTTTACCTAAGCTTGACTATG
GTACGACTTGGTATTCCATGTTGTGAAATTCATACTGGAGATGTCTACCTC
ORF - retro_ogar_2706 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.49 % |
| Parental protein coverage: | 54.86 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MELDDLPELQAVQSDPNQSAMYQLSSDVSHQEYPRTSWN-QNTSDISENTYRENEVDWLTELANIATSPQ |
| ME.D.L.ELQAV.S...QSAMYQLS.D.S.QEY.R.S.N.QN.SDI.ENT..E.EV.WLTEL.NI.TSPQ | |
| Retrocopy | METDELLELQAV*SGLTQSAMYQLS*DISDQEYLRPS*N>QNISDIPENTGCETEVVWLTELVNITTSPQ |
| Parental | SPLMQCSFYNRSS-PVHIIATSKSLHSYARPPPVSSS-SKSEPAFP-HHHWKE-ETPGRHERANSESESG |
| S.LMQCSFYN.SS.PVHI.ATSK....YA.PPP.SSS.SKSEPAFP.HH...E..T..........SES. | |
| Retrocopy | SSLMQCSFYNTSSSPVHIRATSKFTFLYA-PPPGSSS<SKSEPAFPHHHWKEE<NTSEA*KGKHNKSESS |
| Parental | IFCMSSLSDDDDLGWCNSWPSTVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQVST-HKGY |
| ...MS.LSD.DDL.WCNSWPSTVWH.FLKGT.L.FH.GSNKE..D.EDFARAE.CD.EE.LQ.ST..KGY | |
| Retrocopy | VLHMSTLSDNDDLRWCNSWPSTVWHYFLKGTKLYFHEGSNKERRDAEDFARAESCDEEEGLQMSTQNKGY |
| Parental | GSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCE |
| ..DGLKLLSHEES.SF.ESVLKLTFDPGT.EDG.LT..C.LDHPFYVKNKG.SSFY.SLT.V..GIPCCE | |
| Retrocopy | SCDGLKLLSHEESTSFAESVLKLTFDPGTAEDGVLTMVCRLDHPFYVKNKG*SSFYLSLTMVRLGIPCCE |
| Parental | IHIGDVCL |
| IH.GDV.L | |
| Retrocopy | IHTGDVYL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Otolemur garnettii was not studied using RNA-Seq expression data.
Otolemur garnettii was not studied using ChIP-Seq data.
Otolemur garnettii was not studied using EST data.
Otolemur garnettii was not studied using FANTOM5 data.
retro_ogar_2706 was not experimentally validated.
Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000013102 | 1 retrocopy |
retro_ogar_2706 ,
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