RetrogeneDB ID: | retro_ocun_1254 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 4:38670300..38671040(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DYNC1LI2 | ||
| Ensembl ID: | ENSOCUG00000006143 | ||
| Aliases: | None | ||
| Description: | dynein, cytoplasmic 1, light intermediate chain 2 [Source:HGNC Symbol;Acc:2966] |
Retrocopy-Parental alignment summary:
>retro_ocun_1254
CGTGAGCCCATGGATAAAATGAAAATTCCGCCAGAAGGAATGAGGGAGCGGAACGGAAGTTTGGGAAATATTTCCAAGGC
TATATCAAGTTTGAGGAAGGTTGTCAAGATTCCCCACAGCTGAAAGGGCCTCTGCCCACAGGCTCGGGTGAGGAGCATGC
TGCCTTGCCCCTGGTGAAAACGTGCGAACTCACAACATGGGGGCCCTGCGTTGGCAGTGTGCGCAAAGTGGGATGCAGTG
AGCATCCCAAAGAAGGGGCAGGACTACAGCCAGCAGCACCTGGACTTCATCCAGTCTCACCTGTGCAGGTTCTGCCTCCA
GGATGGGGCTGCCTTGATGCACACAATCAGTGAAGAAAGAGGAAAACCTCAACTTGTTGCATAAGTACCTTGTGCATAAA
ACATGTGGGTTCCATTTTACCACACCTGCCTTAGCTGTGGAAAAGGGTGCAGTTTTTATACCTGCAGGCTGGGATGGTAA
AAAGAATATAGCTATTATTACATGAAAACTTCACAACCGTGAAGCCCAAAGATGCATATGAAGACTTTGTCCTGAAACCT
GCTGTGAGAAAGCTGGTCCACGACAAAGGGTTGGCAGTAGAGGGTATGCAGGTGTTCCTAAGGAAGCAATAATCACCCCT
TGCGTAGCAGCCAGCCATGCCCACGCCAGCGTCGCAATCCTCTGCAGGAGGACCTGCTGGCTCTCCAAGTACCCAGGGCC
CGGGCGGGCCAGCCAGTATG
ORF - retro_ocun_1254 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.24 % |
| Parental protein coverage: | 50.2 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | REHIDKMKIPPEEMRE-LERKFVKDFQDYIEPEEGCQGSPQRRGPLTAGSDEESVALPL-GDNVLTHNLG |
| RE..DKMKIPPE.MRE..ERKF.K.FQ.YI..EEGCQ.SPQ..GPL..GS.EE..ALPL.G.NV.THN.G | |
| Retrocopy | REPMDKMKIPPEGMRE<AERKFGKYFQGYIKFEEGCQDSPQLKGPLPTGSGEEHAALPL<GENVRTHNMG |
| Parental | I-PVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYT-SVKEEKNLDLLYKYIVHKTY |
| ..P.L.VC.K.DAVS...K..DY...HLDFIQSHL.RFCLQ.GAAL..T.SVK.E.NL.LL.KY.VHKT. | |
| Retrocopy | A<PALAVCAKWDAVSIPKKGQDYSQQHLDFIQSHLCRFCLQDGAALMHT>SVKKEENLNLLHKYLVHKTC |
| Parental | GFHFTTPALVVEKDAVFIPAGWDNEKKIAI-LHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQV |
| GFHFTTPAL.VEK.AVFIPAGWD..K.IAI.LHENFTTVKP.DAYEDF..KP.VRKLVHDK.LA.E..QV | |
| Retrocopy | GFHFTTPALAVEKGAVFIPAGWDGKKNIAI>LHENFTTVKPKDAYEDFVLKPAVRKLVHDKGLAVEGMQV |
| Parental | FLMKQQSLLAKQPVTPTRASESPARGPSGSPRTQGRGGPASV |
| FL.KQ.S.LA.QP..PT.AS.S.A.GP.GSP.TQG.GGPAS. | |
| Retrocopy | FLRKQ*SPLA*QPAMPTPASQSSAGGPAGSPSTQGPGGPASM |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 151 .88 RPM |
| SRP017611_kidney | 0 .00 RPM | 53 .31 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .43 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1254 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1254 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1254 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000006143 | 1 retrocopy |
retro_ocun_1254 ,
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