RetrogeneDB ID: | retro_cfam_1637 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 38:16052564..16053727(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MUS81 | ||
| Ensembl ID: | ENSCAFG00000013216 | ||
| Aliases: | None | ||
| Description: | MUS81 structure-specific endonuclease subunit [Source:HGNC Symbol;Acc:29814] |
Retrocopy-Parental alignment summary:
>retro_cfam_1637
CAGAGATGTGCCCAGGAAGCTCCCAGGGTGGCTCTTGGGAGTACTCGACCCTGGCCAGCCCTCCGCTCCCTCCTCCACAG
GAACCTGGTTCTCAGGACACACCAGCCAGCCAGGTACTCGCTGACTCCGGAGGGTCTGGAGCTGGCCCAGAAGCTGGCTG
AGTCAGAGGGCCTGAGCTTACTGGATGTGGGCTTCAGGCCAGAGGAGCCCCCTGGGAAAGAGCCAGAAGTGCCAGGAGTG
GCCTCTGCTGAGTTTGGTGCTAGTGAAGGGAGTGTCCAGCAGCTGCCACTGGAGCTTGGGCCTGGAGAGTACAGGGTGCT
GTTGTGTGTGGACGTTGGCAAAGCCAAGGGGGCAGGGCACAGGCCAGAATTGCTCCTGGAGCTACAGCGGCTGCATGTGA
CCCACGTAGTGCGCAAGTTGCATGTCGGGGACTTTGTGTGGGTGGCTCAGGAGACCAGGCCCAGAGACCCAGCAAGACCT
GGGGAGCTCGTCCCGGACCACATCGTGGAGCCAAGCGGCTAGATGATCTGTGCAGCAGCATCACAGATGGCCGCTTCCGA
GAGCAGAAGTTCCGGCTGAAGCGCTGTGGTCTGGGGCACAGAGTACACCTGGTGGAGGAGCATGGCTCTGCAAACCACCT
TAGCCTTCCTGAGGGCACGCTGCTGCAGGCTGTCACCAACACTCAGGTCGTCGATGGCTTCTTTGCGAAGCGCACAGCAG
ACATCAAGGAGTCAGCTGCCTACCTGGCCCTCTAGACGCGGGGCTTGCAGAGGCTCTACCAGGGCCATACCCTACGCAGT
CGCCCCTGGGGAACCTCAGGGGATCCTGAATCAAGGCCTGGGCCCTCCCCACAGCCTCTCTGCTCACTCCTCACCTTCAG
TGACTTCAGCTCGGGAGCCACGAAGAACAAGGCCCAGTGTGTGCACGAGGTGTTCGCCAGGCAGCTGACGCAGGTGCGGG
GAGTGAGCGGGGAGAAGGCAGCAGCCATAGTGGGCCAGTACAGCACCCCTGCCAGCCTCCTGGCAGCCTGTGACGCCTGT
GTCACCCCCAAGGAACAGGAGATGCTGCTGAGCACCATCAAGTGTGGTCGACTGCAGAGGAATCTGGGGCCTGCTCTGAG
CAGAATCTTTTCCCAGCTCTACTGCTGCTACAGCCCTCTGACC
ORF - retro_cfam_1637 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.57 % |
| Parental protein coverage: | 70.29 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QRCAQKAPRVALGSTRPWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEGLSSLDVGFRPEEP |
| QRCAQ.APRVALGSTRPWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEGLS.LDVGFRPEEP | |
| Retrocopy | QRCAQEAPRVALGSTRPWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEGLSLLDVGFRPEEP |
| Parental | PGKEPEVPGAASAELGASEGSVQQLPLELGPGEYRVLLCVDVGEAKGAGHKPKLLLELQRLHVTHVVRKL |
| PGKEPEVPG.ASAE.GASEGSVQQLPLELGPGEYRVLLCVDVG.AKGAGH.P.LLLELQRLHVTHVVRKL | |
| Retrocopy | PGKEPEVPGVASAEFGASEGSVQQLPLELGPGEYRVLLCVDVGKAKGAGHRPELLLELQRLHVTHVVRKL |
| Parental | HVGDFVWVAQETRPRDPARPGELVLDHIVE-RKRLDDLCSSIIDGRFREQKFRLKRCGLGHRVYLVEEHG |
| HVGDFVWVAQETRPRDPARPGELV.DHIVE..KRLDDLCSSI.DGRFREQKFRLKRCGLGHRV.LVEEHG | |
| Retrocopy | HVGDFVWVAQETRPRDPARPGELVPDHIVE<AKRLDDLCSSITDGRFREQKFRLKRCGLGHRVHLVEEHG |
| Parental | SAHHLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTLGLQRLYQGHTLRSRPWGTSGDPESR |
| SA.HLSLPE.TLLQAVTNTQV.DGFF.KRTADIKESAAYLAL.T.GLQRLYQGHTLRSRPWGTSGDPESR | |
| Retrocopy | SANHLSLPEGTLLQAVTNTQVVDGFFAKRTADIKESAAYLAL*TRGLQRLYQGHTLRSRPWGTSGDPESR |
| Parental | PGPSPHPLCSLLTFSDFNAGAMKNKAQCVQEVFARQLMQVRGVSGEKAAAIVGQYSTPASLLAAYDACVT |
| PGPSP.PLCSLLTFSDF..GA.KNKAQCV.EVFARQL.QVRGVSGEKAAAIVGQYSTPASLLAA.DACVT | |
| Retrocopy | PGPSPQPLCSLLTFSDFSSGATKNKAQCVHEVFARQLTQVRGVSGEKAAAIVGQYSTPASLLAACDACVT |
| Parental | PKEQEMLLSTIKCGRLQRNLGPALSRIFSQLYCCYSPLT |
| PKEQEMLLSTIKCGRLQRNLGPALSRIFSQLYCCYSPLT | |
| Retrocopy | PKEQEMLLSTIKCGRLQRNLGPALSRIFSQLYCCYSPLT |
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 .04 RPM | 32 .63 RPM |
| SRP017611_brain | 0 .00 RPM | 21 .67 RPM |
| SRP017611_kidney | 0 .00 RPM | 24 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 15 .88 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1637 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1637 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1637 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 | ENSCAFG00000013216 | 1 retrocopy |
retro_cfam_1637 ,
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