RetrogeneDB ID: | retro_cfam_1083 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 22:49570066..49571084(-) | ||
| Located in intron of: | ENSCAFG00000005809 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GNB1 | ||
| Ensembl ID: | ENSCAFG00000019216 | ||
| Aliases: | None | ||
| Description: | Canis lupus familiaris guanine nucleotide binding protein (G protein), beta polypeptide 1 (GNB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001003236] |
Retrocopy-Parental alignment summary:
>retro_cfam_1083
ATGAGTGAACTTGACTAGTTATGGCAGGAGGCCGAGCAGCTTAAAAACCAAATTAGGGATGTTAGAAAGGCATGTGCAGA
TGTAACTGTCTCTCAGATCACAAACAACATCGACCCAGTAGGAAGAATCCAGATGCACACACCAGGAGAACGCTGAGGGC
ATTTGGCCAAAACTTATGCCATGCATTGGGGCACAGATTCCAGGCTTCTGGTCAGTGCCTCACAGGATAACAAACTGATC
ATCTGGGATAGCTACGCTACAAACTAGGTCCATGCCAACCCTCTGCGTTCCTCATGGGTCATGACCTGTGCATATGCCCC
TTCTGGGAACTATGTGGCCTGTGGTGGCCTGGATAACATTTGCTCCATTTACAATCTGAAAACTCGTGAAGGGAATGTAC
GTGTGAGCCGTGAACTGGCAGACATACAGGTTATCTGTCCTGCTGCCGCTTCCTGGATGACAATCAGATCATCACCAGCT
CTAGGGACACCACTTGTGCTCTGTGGGACATTGAGACCAGCCAGCAGTCAACCACATTCACTGGACACGCTGGGGATGTT
ATGAGCCCTTCTCTCGCTCCCAACACCAGACTGTTTGTCTCTGGTGCTTGTGATGCATCAGCCAAATTCTGGGATGTGCA
AGAAGGGATGTGCCGGCAAACTTTCACCGGCCACGAGTCCGACATCAATGCCATCTGTTTCTTTCCAAACGGCAATGCAT
TTGCACTGGCTTGGATGATGCCACCTGTAGGCTGTTCAACCTTCGTGCACAGCAGGAGGTCATGACTTATTCCCATGACA
ACATCATCTGTGGGATCACCTCGGTGTCTTTCTCCAAGAGCGGGTGCCTCCTCCTCACAGGGTACGATGACTTCAACTGC
AATGTGTGGGACGCACTCAAGGCCGACAGAGCAGGTGTCTTGGCTGGGAATGACAACCGTGTCAGCTGCCTGGGGGTGAC
TGACGATGGGATGGCTACGGCGACACGGTCCTGGGATAGCTTCCTCAAGATCTGGAAC
ORF - retro_cfam_1083 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.18 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLL |
| MSELD.L.QEAEQLKNQIRD.RKACAD.T.SQITNNIDPVGRIQM.T.....GHLAK.YAMHWGTDSRLL | |
| Retrocopy | MSELD*LWQEAEQLKNQIRDVRKACADVTVSQITNNIDPVGRIQMHTPGER*GHLAKTYAMHWGTDSRLL |
| Parental | VSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA |
| VSASQD.KLIIWDSY.TN.VHA.PLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA | |
| Retrocopy | VSASQDNKLIIWDSYATN*VHANPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA |
| Parental | G-HTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAK |
| ..HTGYLSCCRFLDDNQI.TSS.DTTCALWDIET.QQ.TTFTGH.GDVMS.SLAP.TRLFVSGACDASAK | |
| Retrocopy | D<HTGYLSCCRFLDDNQIITSSRDTTCALWDIETSQQSTTFTGHAGDVMSPSLAPNTRLFVSGACDASAK |
| Parental | LWDVREGMCRQTFTGHESDINAICFFPNGNAFA-TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSF |
| .WDV.EGMCRQTFTGHESDINAICFFPNGNAFA.TG.DDATCRLF.LRA.QE.MTYSHDNIICGITSVSF | |
| Retrocopy | FWDVQEGMCRQTFTGHESDINAICFFPNGNAFA<TGLDDATCRLFNLRAQQEVMTYSHDNIICGITSVSF |
| Parental | SKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN |
| SKSG.LLL.GYDDFNCNVWDALKADRAGVLAG.DNRVSCLGVTDDGMA.AT.SWDSFLKIWN | |
| Retrocopy | SKSGCLLLTGYDDFNCNVWDALKADRAGVLAGNDNRVSCLGVTDDGMATATRSWDSFLKIWN |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 420 .79 RPM |
| SRP017611_brain | 0 .48 RPM | 302 .48 RPM |
| SRP017611_kidney | 0 .40 RPM | 193 .95 RPM |
| SRP017611_liver | 0 .44 RPM | 64 .10 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1083 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1083 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1083 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019216 | 1 retrocopy |
retro_cfam_1083 ,
|
| Echinops telfairi | ENSETEG00000020012 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000016638 | 1 retrocopy |