RetrogeneDB ID: | retro_rnor_2476 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 7:102505121..102505858(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Gcm1 | ||
| Ensembl ID: | ENSRNOG00000007932 | ||
| Aliases: | Gcm1, Gcma | ||
| Description: | Chorion-specific transcription factor GCMa [Source:UniProtKB/Swiss-Prot;Acc:Q9Z288] |
Retrocopy-Parental alignment summary:
>retro_rnor_2476
ATGGAACTGGACAACTGTGATCCTGAAGACAAGAGATACTGAGCTGGGATATTAACGACATGAAGCTGCCTCAGAATGTG
AAGAAGACTGACTGGTTCCAGGAGTGGCCAGACTCCTATGTGAAACACAGCTACAGCTCAGACGACAGGAGCGCACAGCA
CCATCTGAGCAGCTGGGCCATGCGCAACAGCAACAACCACAACTCCCAGATCCTCAAGAAGTCGTGCCTGGGGGTAGTGG
TGTGCACCAGGAACTGTTCCACGGAGAAAGGCCGCAAGATTTATCTGAGACCCACCATCTGTGACAAAGCCAGGCAGAAG
CAGCAGAGGAAAAGCTGTCCCAACTGCAATGGACCCCTGAAACTAATTCCCTGCAGAGGCCACGGCGGCTTCCCGATCAC
CAACTTCTAGAGGCATGACAGACGCTTCATCTTTTTCTAGTCCAAAGGAGAGCACGATCATCCCAGGCCGGAGACCAATC
TAGAAACAGAGGCAAGAAGAGCAGTGAAGAAAGTGCACATGGCCTCTGCCTCCAGCTCCTTACGGATGAAGGGGAGACCA
GAAATGAAGGGTCTTCCAGGTGAAATCCCGAGTCAGGGAAGTTTACCTTTAACTGGGTCATTCCAGGAAGGCGTCCAACT
GCCCAGCGGTTATAGCACACCTTTAATAGCTAACGCTCCCCAGCAGAACTCCCTGAATGATTGCCTGTCCTTCCCCAAGA
GTTATGACTTGGGGGGA
ORF - retro_rnor_2476 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.31 % |
| Parental protein coverage: | 56.42 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MELDDFDPEDK-EILSWDINDMKLPQNVKKTDWFQEWPDSYVKHIYSSDDRSAQRHLSSWAMRNTNNHNS |
| MELD..DPEDK.EILSWDINDMKLPQNVKKTDWFQEWPDSYVKH.YSSDDRSAQ.HLSSWAMRN.NNHNS | |
| Retrocopy | MELDNCDPEDK<EILSWDINDMKLPQNVKKTDWFQEWPDSYVKHSYSSDDRSAQHHLSSWAMRNSNNHNS |
| Parental | RILKKSCLGVVVCSRDCSTEEGRKIYLRPAICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPVTNFWRH |
| .ILKKSCLGVVVC.R.CSTE.GRKIYLRP.ICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFP.TNF.RH | |
| Retrocopy | QILKKSCLGVVVCTRNCSTEKGRKIYLRPTICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPITNF*RH |
| Parental | DGRFIFFQSKGEHDHPRPETKLEAEARRAMKKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLTWSFQ |
| D.RFIFF.SKGEHDHPRPET.LE.EARRA.KKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLT.SFQ | |
| Retrocopy | DRRFIFF*SKGEHDHPRPETNLETEARRAVKKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLTGSFQ |
| Parental | EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG |
| EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG | |
| Retrocopy | EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG |
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 | 1 .65 RPM | 0 .29 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .68 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2476 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2476 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2476 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 | ENSCAFG00000002273 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000007932 | 1 retrocopy |
retro_rnor_2476 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000014763 | 1 retrocopy |