RetrogeneDB ID: | retro_cfam_2077 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:49385846..49386650(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GTF2A1L | ||
| Ensembl ID: | ENSCAFG00000002692 | ||
| Aliases: | None | ||
| Description: | Canis lupus familiaris general transcription factor IIA, 1-like (GTF2A1L), mRNA. [Source:RefSeq mRNA;Acc:NM_001204843] |
Retrocopy-Parental alignment summary:
>retro_cfam_2077
CTAGTGACCTCAAGCTCTAGTGCAAGCTTCACTTTTTCTGGATATCCTATTCATGTGCCAGCAGGTGTGACACTGCAGAC
TGCATCTGGTCACGTTTATAAAGCCAATGTACCAATTATGGTGACACAGACTTCTGGAAGAGCAAGTATTCTACATCCAA
TTCAGCAAGTATTTCAGCAGCTGGGGCAGCCTCCAATAATCCAGACCAGTGTTCCACAATTGAACCCATGTTCTCTCCAC
GCCACTACTGAAAAATCACAGAGAATAGAAACTGTGCTCCAGCAACCCACAATTCTTCATTCTGGGACAGTGGATAGGAA
ACATTTAGAAAATGCCACGAGTGATATATTTGCACCTCCTGCAAATGAGCGTGAAATCATGTCTGAAGCCTTGTAGAGTC
AGCCGGAAAGTTCGCAGTACATCAGTCTTCCAGGTGTTGTGTTTCCTCCACAGGTCTCTCAGACAGATTCCCAAGTGGAG
CCTGTGCTCAGTGTTTCAGGCAGCATGACTCAAAATCTGAATGGTAGGCCCTTCTCCACCAGCCAACAGGGGGCCCAGCA
CCGGCACATGTCTGATACTCAGCTTCATGTTCTTAAAAATAGGATGTTTGGATGTGATTCTATAAAGCAACAAAGAAATA
CAGAGGAGCCCAGCAGCCTACCTGTCTCAGAGAAGGATTCTAATTCTCAGATGGATTTAAGCATTCAGGTAATTGATGAT
ATTAATGAAATAATTCAAATAGATGGAACCGGTGATACATTTTCCAATGATGAAATAGGAAGAACAAGAGATGTAGATGA
GAAC
ORF - retro_cfam_2077 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.9 % |
| Parental protein coverage: | 56.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LGTSSSSASFTLSGYPIHVPAGVTLQTASGHLYKVNVPIMVTQTSGRASILHPIQQVFQQLGQPPIIQTS |
| L.TSSSSASFT.SGYPIHVPAGVTLQTASGH.YK.NVPIMVTQTSGRASILHPIQQVFQQLGQPPIIQTS | |
| Retrocopy | LVTSSSSASFTFSGYPIHVPAGVTLQTASGHVYKANVPIMVTQTSGRASILHPIQQVFQQLGQPPIIQTS |
| Parental | VPQLNPCSLHATTEKSQRIETVLQQPTILHSGTVDRKHLENATSDILAPPANEREIMSEALLSQPESSQY |
| VPQLNPCSLHATTEKSQRIETVLQQPTILHSGTVDRKHLENATSDI.APPANEREIMSEAL.SQPESSQY | |
| Retrocopy | VPQLNPCSLHATTEKSQRIETVLQQPTILHSGTVDRKHLENATSDIFAPPANEREIMSEAL*SQPESSQY |
| Parental | ISLPGVVFPPQVSQTDSQVEPVLSVSGSMTQNLNGRPFSTSQQGAQHRHMSDTQLHVLKNRMFGCDSIKQ |
| ISLPGVVFPPQVSQTDSQVEPVLSVSGSMTQNLNGRPFSTSQQGAQHRHMSDTQLHVLKNRMFGCDSIKQ | |
| Retrocopy | ISLPGVVFPPQVSQTDSQVEPVLSVSGSMTQNLNGRPFSTSQQGAQHRHMSDTQLHVLKNRMFGCDSIKQ |
| Parental | QRNTEEPSNLPVSEKDSNSQMDLSIQVTDDINEIIQIDGTGDASSNDEIGSTRDVDEN |
| QRNTEEPS.LPVSEKDSNSQMDLSIQV.DDINEIIQIDGTGD..SNDEIG.TRDVDEN | |
| Retrocopy | QRNTEEPSSLPVSEKDSNSQMDLSIQVIDDINEIIQIDGTGDTFSNDEIGRTRDVDEN |
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 .42 RPM | 58 .63 RPM |
| SRP017611_brain | 0 .64 RPM | 15 .96 RPM |
| SRP017611_kidney | 0 .20 RPM | 28 .26 RPM |
| SRP017611_liver | 0 .15 RPM | 9 .57 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2077 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2077 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2077 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000002692 | 1 retrocopy |
retro_cfam_2077 ,
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