RetrogeneDB ID: | retro_cfam_520 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 12:37199166..37200278(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BACE2 | ||
| Ensembl ID: | ENSCAFG00000010157 | ||
| Aliases: | None | ||
| Description: | beta-site APP-cleaving enzyme 2 [Source:HGNC Symbol;Acc:934] |
Retrocopy-Parental alignment summary:
>retro_cfam_520
GCAGACAAGTCCAGTACGTACCGCTCCAAGGGCTTTGATGTCACTGCGAACTACACGCAAGGGAGCTGGACTGACATCGT
CGGGGAGGACTTTGTCACCATCCCCAAAGGCTTCAACAGCTCCTTCTTTGTCAACATTGCCACTATCTTTGAGTCCGAGA
ATTTCTTTCTGCCTGGTATCAAATGGAATGAGACACTTGAACTCGCATATGCTGCTCTGGCCAAGCCATCCAGTTCCCTG
GAGACTTTCTTTGATTCTCTGGCGGCGCAGGCGAAGATCCCCCAACGTCTTCTCCATGCAGATGTGGGGGGCGGGGCTGC
CCGTAGCTGGATCTGGTACCAACGGAGGTAGTCTTGTCCTGGGTGGAACTGAACCGAGTTTGTACAAAGGAGACATCTGG
TATACCCGTATTAAGGACGAGTGGTATTATCAGATAGAAATTCTGAAGTTGGAAATTGGAGGCCAGAGTCTGAATCTGGA
CTGCAGAGAGTATAACGCAGACAAGGCCATCGTGGATAGCGGTACCACGCTTCTGCGCCTGCCCCAGAAGGTGTTCAATG
TGGTGGTTGAAGCCGTGACCCGCACGTCTCTTGATTCCAGAATTCTCTGATGGTTTCTGGACTGGGTCCCAGCTGGCTTG
CTGGACGAATTCGGAGATACCTTGGTCTTACTTCCCTAAAATCTCCATCTACCTAGAGACGAGAACTCCAGCCAGTCATT
CGGCATAACCATCCTGCCTCAGCTGTACGTCCAGCCCATGATGGGGGCTGGCCTGAATTATAAATGTTACCGATTCGGCA
TCTCACCTTCCACGAACGCGCTGGTGATTGGTGCTACCGTGATGGAGGGCTTCTACGTGGTCTTCGACAGAGCTTGGAAG
AGGGTGGGCTTTGCAGCAAGCCCCTGTGCAGAAATTGCAGGTGCTCCAGTGTCTGAAATTTCTGGGCCTTTCTCGACAGA
CAACATAGCCAGCAACTGCGTCCCCGCCCTGTCTTTGAATGATCCCATTTTGTGGATCGTCTCCTATACTCTCTTGAGCG
TGTGTGGAATCATCCTTCTTCTCCTAATCATCCTGCTGCTACTTCCCTTCCCAGTGTCGGCACCTGCCCCGT
ORF - retro_cfam_520 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.44 % |
| Parental protein coverage: | 88.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | ADRSSTYRSKGFDVTVKYTQGSWTGFVGEDFVTIPKGFNSSFLVNIATIFESENFFLPGIKWNGILGLAY |
| AD.SSTYRSKGFDVT..YTQGSWT..VGEDFVTIPKGFNSSF.VNIATIFESENFFLPGIKWN..L.LAY | |
| Retrocopy | ADKSSTYRSKGFDVTANYTQGSWTDIVGEDFVTIPKGFNSSFFVNIATIFESENFFLPGIKWNETLELAY |
| Parental | AALAKPSSSLETFFDSLVAQAKIP-NVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKE |
| AALAKPSSSLETFFDSL.AQAKIP.NVFSMQM.GAGLPVAGSGTNGGSLVLGG.EPSLYKGDIWYT.IK. | |
| Retrocopy | AALAKPSSSLETFFDSLAAQAKIP>NVFSMQMWGAGLPVAGSGTNGGSLVLGGTEPSLYKGDIWYTRIKD |
| Parental | EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFNAVVEAVARTSL-IPEFSDGFWTG |
| EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFN.VVEAV.RTSL.IPEFSDGFWTG | |
| Retrocopy | EWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFNVVVEAVTRTSL>IPEFSDGFWTG |
| Parental | SQLACWTNSETPWSYFPKISIYL-RDENSSQSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIG |
| SQLACWTNSE.PWSYFPKISIYL.RDENSSQSF.ITILPQLY.QPMMGAGLNY.CYRFGISPSTNALVIG | |
| Retrocopy | SQLACWTNSEIPWSYFPKISIYL<RDENSSQSFGITILPQLYVQPMMGAGLNYKCYRFGISPSTNALVIG |
| Parental | ATVMEGFYVVFDRARKRVGFAASPCAEIAGAPVSEISGPFSTDDIASNCVPALPLNEPILWIVSYTLMSV |
| ATVMEGFYVVFDRA.KRVGFAASPCAEIAGAPVSEISGPFSTD.IASNCVPAL.LN.PILWIVSYTL.SV | |
| Retrocopy | ATVMEGFYVVFDRAWKRVGFAASPCAEIAGAPVSEISGPFSTDNIASNCVPALSLNDPILWIVSYTLLSV |
| Parental | CGIILLILIVLLLLPF-RCRHLPR |
| CGIILL.LI.LLLLPF..CRHLPR | |
| Retrocopy | CGIILLLLIILLLLPF>QCRHLPR |
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 | 7 .69 RPM |
| SRP017611_brain | 0 .00 RPM | 8 .57 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .02 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .13 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_520 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_520 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_520 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 | ENSCAFG00000010157 | 1 retrocopy |
retro_cfam_520 ,
|
| Ciona intestinalis | ENSCING00000005258 | 1 retrocopy | |
| Ciona savignyi | ENSCSAVG00000008457 | 1 retrocopy |