RetrogeneDB ID: | retro_cpor_1066 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_43:568454..569585(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000010178 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PJA2 | ||
| Ensembl ID: | ENSCPOG00000014595 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1066
TTTAATAGGCATGAAACTAAACAGAAAACTGTTCAGAGATGGAGGGAGGCTTTGGAAGTTGAGGAATGTGGCTCAGATGA
CCGCTTAATAAAATGTGAAGAATATGATGATGGAGAGCATGACTGTATATTCTTGGATCTTCCTTATGCAAGAGTCACAC
CACAGGAAACAGAAAACCATATAACATCTGAAAATAGAGCTGCAGCAGGAAAGCAAGAAGTTCGGGACAGTGCCTTTTGG
AATGGCTGCAGAGATTATTACCAGCTCTTTGACAGAGATGAAGATAGTTCAGAATGTAGTGATGGGGAGTGGTCCTGCTT
CTTTGCCTCATCGATTTTCTGGTTCAGAAAAAGATCAGTCCTCAAGTGATGAAAGCTGGAGACTCTGCCAGGAAAAGATA
AGAATGAACCTGAGCTGCAGAGTGATAGCAGTGGCCCCGAAGAAGAAAACCAAGAATTATCTCTGCAGGAAGGGGAGCAG
ACATCCTTGGAAGAGGGAGAGATTCCTTGGCCGCGGTACAGTGAAGTCAATGAAAGCAGCAATGATGAGGGAAATGAGCC
CGCCAATGAATTTCCACAGCCAGAAGCTTTCATGTTGGACAGTAACAACAATCTTGAGGATGACTCCAGTGTGAGTGAAA
ACTTGGATGTGGATTGGAGTTTATTTGACGGCTTTGCAGATGGCCTTGGAGTTGCTGAAGCTATTTCTTATGTGGATCCT
CAGTTCCTCACCTGCATGGCACTGGAAGAGCGCTTAGCCCAGGCTATGAAGACTGCACTGGCACATTTAGAGTCCCTGGC
AGTGGATGTGGAGGTGGCCAATCCACCAGCCAGTAAGGAGAGCATCGATGTCCTGCCAGAGACCCTTGTTCTTGAAGATC
ACACTGCTATTGGTCAGGAGCAGTGCTGTCCAATCTGTTGCAGTGAATATATAAAGAATGATATAGCAACAGAGTTACCC
TGTCACTGTTTCTTTCACAAACCTTGCGTCTCAATTTGGCTACAGAAGTCGGGAACATGCCCTGTGTGCTGCTGCCATTT
CCCACCTGCAGTTATTGAAACGTCTGCAGCTGGTTCCTCTGAGTTTGAGCCTGATGCCCCACCTTCAACTGACAGCACTG
CAGAAGCCCCC
ORF - retro_cpor_1066 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.14 % |
| Parental protein coverage: | 53.48 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | FNRHEAKQRSVQRWREALEVEECASDDPLIKCEEYDDGEHDCMFLDLPYARVTPQETENHITSESRAAAG |
| FNRHE.KQ..VQRWREALEVEEC.SDD.LIKCEEYDDGEHDC.FLDLPYARVTPQETENHITSE.RAAAG | |
| Retrocopy | FNRHETKQKTVQRWREALEVEECGSDDRLIKCEEYDDGEHDCIFLDLPYARVTPQETENHITSENRAAAG |
| Parental | RQEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS-ASLPHRFSGSEKDQSSSDESW-ETLPGKDENEPE |
| .QEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS.ASLPHRFSGSEKDQSSSDESW.ETLPGKD.NEPE | |
| Retrocopy | KQEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS>ASLPHRFSGSEKDQSSSDESW<ETLPGKDKNEPE |
| Parental | LQSDSSGPEEENQELSLQEGEQTSLEEGEIPWLQYSEVNESSSDEGNEPANEFAQPEAFMLDGNNNLEDD |
| LQSDSSGPEEENQELSLQEGEQTSLEEGEIPW..YSEVNESS.DEGNEPANEF.QPEAFMLD.NNNLEDD | |
| Retrocopy | LQSDSSGPEEENQELSLQEGEQTSLEEGEIPWPRYSEVNESSNDEGNEPANEFPQPEAFMLDSNNNLEDD |
| Parental | SSVSEDLDVDWSLFDGFADGLGVAEAISYVDPQFLTYMALEERLAQAMETALAHLESLAVDVEVANPPAS |
| SSVSE.LDVDWSLFDGFADGLGVAEAISYVDPQFLT.MALEERLAQAM.TALAHLESLAVDVEVANPPAS | |
| Retrocopy | SSVSENLDVDWSLFDGFADGLGVAEAISYVDPQFLTCMALEERLAQAMKTALAHLESLAVDVEVANPPAS |
| Parental | KESIDGLPETLVLEDHTAIGQEQCCPICCSEYIKDDIATELPCHHFFHKPCVSIWLQKSGTCPVCRRHFP |
| KESID.LPETLVLEDHTAIGQEQCCPICCSEYIK.DIATELPCH.FFHKPCVSIWLQKSGTCPVC..HFP | |
| Retrocopy | KESIDVLPETLVLEDHTAIGQEQCCPICCSEYIKNDIATELPCHCFFHKPCVSIWLQKSGTCPVCCCHFP |
| Parental | PAVIEASAAGSSELEPDAPPSTDSTAEAP |
| PAVIE.SAAGSSE.EPDAPPSTDSTAEAP | |
| Retrocopy | PAVIETSAAGSSEFEPDAPPSTDSTAEAP |
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 .12 RPM | 290 .80 RPM |
| SRP017611_kidney | 0 .00 RPM | 92 .75 RPM |
| SRP017611_liver | 0 .00 RPM | 63 .72 RPM |
| SRP040447_lung | 0 .00 RPM | 74 .45 RPM |
| SRP040447_skeletal_muscle | 0 .03 RPM | 38 .24 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1066 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1066 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000014595 | 1 retrocopy |
retro_cpor_1066 ,
|