RetrogeneDB ID: | retro_cjac_2224 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:28916339..28917434(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000032090 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CRY1 | ||
| Ensembl ID: | ENSCJAG00000015099 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2224
TTATCCTCTGCAGTGTGGCCAGGCGAAGAAATTGAAGCACTTACTCATTTGGAAAGAAAAGCTTGGGTGGCAAACTTTGA
AAGACCTTGAATAAATGCAAACTCTCTGCTTGGAAGCCCTACTGGACTTGGTCCCTATCTCCGATTTGGCTGTTTGTCAT
GTCGGCTGTTTTACTTCCAACTAACAGATCTCTACCAAAGGGTAAAGAAGAGCAGCTCCCCTCCCCTTTCCCTTTATGGG
AAACTGCTATGGCGTGAGTTTTTCTATACCACAGCAACAAATAATCCACGCTTCGATAAAATGGAAGGAAACCCTATCTG
TGTTCAGATTCCTTGGGATAAAAATTCTCAGGCTTTAGCCAAGTGGGCAGAAGGCAGAACAGGCTTTCCCTGGATTGATG
CCATCGTGACTCAGCTTCCTCAGGAGGGCTGGATTCATCATCTAGCCAGGCATGCAGTTGCTTGCTTCCTGACACGGGGA
ACCTGTGGATTAGTTGGGAAGAAGGAATGAAGGTATTTGAAGAATGATTGCTTGATGCAGATTGGAGCATAAATGCTGGA
AGTTGGATGTGGCTGTCTTGTAATTCCTTTATTCAACAGTTTTTTTCACTGCTATTACCTTCTTGGTTTTGGTAGAACAG
ATCCTAATGGAGACTATATCAGGTGTTATTTGCCTGTCCTAAGAGGCTTCCCTGCAAAATATATCGATGATCCCTGGAAT
GCACCAGAAGGTATCCAAAAGGTAGCCAAATGTTTGATAGGAGTTAATTATCCTAAACCAGTGGTGAAGCATGCTGAGGC
AAGTCGTTTGAATATTGAAAGAATGAAACAGATCTATCAGCAGCTTTCACAATATAGAGGACTAGGCCTTCTAGCTTCAG
TACCTTCTAATCCTAGTAGGAATGGAAGCTCCATGGGATATTCTGGAGAAAAAATCCCAGGCTGTAGCAGCAGTGGACGT
TGCTCTCAAGGGAGTGGTATTTTACACTGTGCCCATGGCGACATTCAGCAAACTCACCTATTGAAGCAAGGAAGAAGGTC
AATGAGCACTGGTCTTAGTGGTGGGAAACATCCTAGTCAGGAAGAGGACACACAG
ORF - retro_cjac_2224 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.13 % |
| Parental protein coverage: | 63.2 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LSSAVWPGGETEALTRLERHLERKAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYK |
| LSSAVWPG.E.EALT....HLERKAWVANFERP..NANSLL.SPTGL.PYLRFGCLSCRLFYF.LTDLY. | |
| Retrocopy | LSSAVWPGEEIEALT----HLERKAWVANFERP*INANSLLGSPTGLGPYLRFGCLSCRLFYFQLTDLYQ |
| Parental | KVKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIM |
| .VKK.SSPPLSLYG.LLWREFFYT.ATNNPRFDKMEGNPICVQIPWDKN..ALAKWAEGRTGFPWIDAI. | |
| Retrocopy | RVKKSSSPPLSLYGKLLWREFFYTTATNNPRFDKMEGNPICVQIPWDKNSQALAKWAEGRTGFPWIDAIV |
| Parental | TQLRQEGWIHHLARHAVACFLTR-GDLWISWEEGMKVFEELLLDADWSINAGSWMWLSCSSFFQQ-FFHC |
| TQL.QEGWIHHLARHAVACFLTR.G.LWISWEEGMKVFEE.LLDADWSINAGSWMWLSC.SF.QQ.FFHC | |
| Retrocopy | TQLPQEGWIHHLARHAVACFLTR<GNLWISWEEGMKVFEE*LLDADWSINAGSWMWLSCNSFIQQ>FFHC |
| Parental | YCPVGFGRRTDPNGDYIRRRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNI |
| Y...GFG.RTDPNGDYI.R.YLPVLRGFPAKYI.DPWNAPEGIQKVAKCLIGVNYPKP.V.HAEASRLNI | |
| Retrocopy | YYLLGFG-RTDPNGDYI-RCYLPVLRGFPAKYIDDPWNAPEGIQKVAKCLIGVNYPKPVVKHAEASRLNI |
| Parental | ERMKQIYQQLSRYRGLGLLASVPSNPNGNGGFMGYSAENIPGCTSSGSCSQGSGILHCAHGDSQQTHLLK |
| ERMKQIYQQLS.YRGLGLLASVPSNP..NG..MGYS.E.IPGC.SSG.CSQGSGILHCAHGD.QQTHLLK | |
| Retrocopy | ERMKQIYQQLSQYRGLGLLASVPSNPSRNGSSMGYSGEKIPGCSSSGRCSQGSGILHCAHGDIQQTHLLK |
| Parental | QGRSSMSTGISGGKRPSQEEDTQ |
| QGR.SMSTG.SGGK.PSQEEDTQ | |
| Retrocopy | QGRRSMSTGLSGGKHPSQEEDTQ |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 12 .31 RPM |
| SRP051959_heart | 0 .00 RPM | 9 .56 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .08 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .52 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .62 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 11 .94 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 12 .71 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .47 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2224 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2224 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2224 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015099 | 3 retrocopies |
retro_cjac_2223, retro_cjac_2224 , retro_cjac_3842,
|