RetrogeneDB ID: | retro_rnor_2143 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 5:54392862..54394487(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000023101 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Csgalnact2 | ||
| Ensembl ID: | ENSRNOG00000014713 | ||
| Aliases: | Csgalnact2, Galnact2, RGD1563660 | ||
| Description: | chondroitin sulfate N-acetylgalactosaminyltransferase 2 [Source:RefSeq peptide;Acc:NP_001100086] |
Retrocopy-Parental alignment summary:
>retro_rnor_2143
ATGTCTAGAAGAGGACCGATTCTTCACAGCCGGACCCAGTGGCTGCTGGTGGGCCTTGCTTTGCTTTTCAGTCTAGTATT
ATTTATGTACCTCCTGGAATGTGCCCCCCAGACTGATGGAAATGCTTCTCTCCCTGGTGTGGTTAGAGAAAATTATGGTA
AAGAATATTACCAAGCCCTCCTGCAGGAGCAAGAAGAACATTACCAAACCAGGGCAACCAGTTTGAAACGACAGATTGCC
CAGCTAAAGCAAGAACTACAAGATATGAGTGAGAAGATGAGAGCCTTGCAAGAGAGGAAGAAGCTAGGGGCTAACGGCAT
AGGCGATCAGGGCAACAGAGAGCAGACACCCAGCGACCTCTTAGAGTTTCTTCATTCCCAGATCGACAGAGCTGAAGTCA
GCATAGGGGCCAAACTACCCAGTGAGTATGGAGTCGTTCCCTTTGAAAGTTTTACTTTAATGAAAGTATTTCAGTTGGAA
ATGGGTCTCACGCGCCATCCTGAAGAAAAGCCAGTTAGAAAAGACAAACGAGATGAATTGGTAGAAGTTATTGAAGCTGG
CTTGGAGGTCATTAATAATCCTGATGAAGATGATGAACAGGAAGATGAGGAGGGCCCCCTTGGAGAGAAACTGATATTTA
ATGAAAATGACTTCATAGAAGGCTATTACCGCACTGAGAGAGATAAAGGCACGCACTATGAGCTGTTTTTTAAGAAGGCA
GACCTTATGGCATACAGGCATGTGGCCCTCTTCCGCCCTTTCGGACCTCTCATGAAAGTGAAGAGGAGCTGATTGACATT
ACAAGATCGGTTATTAATATCATTGTGCCGCTTGCTGAGAGGACAGAAGCCTTTTCACAGTTTATGCAGAACTTCAGAGA
TGTTTGTATTCATCAAGACAAGAGAATTCATCTCACCGTTGTGTATTTTGGGAAAGAAGGACTATCTACAGTCAAGTCTA
TTCTAGAATCTGTCTCAAGTGAGTCTAATTTTCACAATTACACCTTGGTCTCATTGAACGAAGAATTTAATCGTGGACGA
GGACTAAATGTGGGTGCCCGAGCTTGGGACAAGGGAGAGGTCTTGATGTTTTTCTGTGATGTTGATATATATTTCTCAGC
TGAATTCCTTAACAGCTGCCGGTTAAATGCTGAGCCAGGTAAAAAAGTGTTTTACCCCGTGGTGTTCAGTCTTTACAACC
CTGCCATCGTCTATGCCAACCAGGAAGTGCCACCTCCCGTGGAGCAGCAGCTGGTTCATAAAAAGGACTCTGGTTTTTGG
AGAGATTTTGGCTTTGGGATGACGTGTCAATATCAATCAGATTTTCTGAGTGTCGGTGGATTCGACATGGAAGTAAAAGG
CTGGGGTGGAGAAGATGTTCATCTTTACCGAAAGTACTTACATGGTGATCTTATTGTGATTCGGACTCCAGTTCCTGGCC
TTTTCCACCTCTGGCATGAGAAACACTGTGCGGACGAGCTGACCCCTGAGCAATACCGAATGTGCATCCAATCCAAAGCC
ATGAACAAGGCCTCTCATTCCCACCTGGGAATGATGGTCTTCAGGGAGGAAATAGAGATGCACCTCCGCAAACAGGCGTA
CAGAACCAACAGCGAGGCCGCTGGG
ORF - retro_rnor_2143 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.71 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSRRGPILHSRTQWLLVGLALLFSLVLFMYLLECAPQTDGNASLPGVVRENYGKEYYQALLQEQEEHYQT |
| MSRRGPILHSRTQWLLVGLALLFSLVLFMYLLECAPQTDGNASLPGVVRENYGKEYYQALLQEQEEHYQT | |
| Retrocopy | MSRRGPILHSRTQWLLVGLALLFSLVLFMYLLECAPQTDGNASLPGVVRENYGKEYYQALLQEQEEHYQT |
| Parental | RATSLKRQIAQLKQELQDMSEKMRALQERKKLGANGIGYQGNREQTPSDLLEFLHSQIDRAEVSIGAKLP |
| RATSLKRQIAQLKQELQDMSEKMRALQERKKLGANGIG.QGNREQTPSDLLEFLHSQIDRAEVSIGAKLP | |
| Retrocopy | RATSLKRQIAQLKQELQDMSEKMRALQERKKLGANGIGDQGNREQTPSDLLEFLHSQIDRAEVSIGAKLP |
| Parental | SEYGVVPFESFTLMKVFQLEMGLTRHPEEKPVRKDKRDELVEVIEAGLEVINNPDEDDEQEDEEGPLGEK |
| SEYGVVPFESFTLMKVFQLEMGLTRHPEEKPVRKDKRDELVEVIEAGLEVINNPDEDDEQEDEEGPLGEK | |
| Retrocopy | SEYGVVPFESFTLMKVFQLEMGLTRHPEEKPVRKDKRDELVEVIEAGLEVINNPDEDDEQEDEEGPLGEK |
| Parental | LIFNENDFIEGYYRTERDKGTHYELFFKKADLMEYRHVTLFRPFGPLMKVK-SELIDITRSVINIIVPLA |
| LIFNENDFIEGYYRTERDKGTHYELFFKKADLM.YRHV.LFRPFGPLMKVK..ELIDITRSVINIIVPLA | |
| Retrocopy | LIFNENDFIEGYYRTERDKGTHYELFFKKADLMAYRHVALFRPFGPLMKVK<EELIDITRSVINIIVPLA |
| Parental | ERTEAFSQFMQNFRDVCIHQDKRIHLTVVYFGKEGLSTVKSILESVSSESNFHNYTLVSLNEEFNRGRGL |
| ERTEAFSQFMQNFRDVCIHQDKRIHLTVVYFGKEGLSTVKSILESVSSESNFHNYTLVSLNEEFNRGRGL | |
| Retrocopy | ERTEAFSQFMQNFRDVCIHQDKRIHLTVVYFGKEGLSTVKSILESVSSESNFHNYTLVSLNEEFNRGRGL |
| Parental | NVGARTWDKGEVLMFFCDVDIYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIVYANQEVPPPVEQQLV |
| NVGAR.WDKGEVLMFFCDVDIYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIVYANQEVPPPVEQQLV | |
| Retrocopy | NVGARAWDKGEVLMFFCDVDIYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIVYANQEVPPPVEQQLV |
| Parental | HKKDSGFWRDFGFGMTCQYQSDFLSVGGFDMEVKGWGGEDVHLYRKYLHGDLIVIRTPVPGLFHLWHEKH |
| HKKDSGFWRDFGFGMTCQYQSDFLSVGGFDMEVKGWGGEDVHLYRKYLHGDLIVIRTPVPGLFHLWHEKH | |
| Retrocopy | HKKDSGFWRDFGFGMTCQYQSDFLSVGGFDMEVKGWGGEDVHLYRKYLHGDLIVIRTPVPGLFHLWHEKH |
| Parental | CADELTPEQYRMCIQSKAMNEASHSHLGMMVFREEIEMHLRKQAYRTNSEAAG |
| CADELTPEQYRMCIQSKAMN.ASHSHLGMMVFREEIEMHLRKQAYRTNSEAAG | |
| Retrocopy | CADELTPEQYRMCIQSKAMNKASHSHLGMMVFREEIEMHLRKQAYRTNSEAAG |
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 | 5 .18 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .28 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .22 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2143 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2143 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2143 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 | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000014713 | 1 retrocopy |
retro_rnor_2143 ,
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