RetrogeneDB ID: | retro_cjac_1033 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:44379611..44380454(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCDC61 | ||
| Ensembl ID: | ENSCJAG00000012104 | ||
| Aliases: | None | ||
| Description: | coiled-coil domain containing 61 [Source:HGNC Symbol;Acc:33629] |
Retrocopy-Parental alignment summary:
>retro_cjac_1033
ATGGGCCAGCTGGCCGGCCTGCAGGTGGACTACGTTTTCCGGGGTGTGGAGCATGCTGTGCAGGTGGTGGTTACCGGGCA
GGTGCTGGAGCTGAAGGTGGAGGACCGGATGACTGTGGTCCAGTGGGGGGGCGAGTTCGATGCCGGCTTCATTGAAAATT
TGACTCACAAGACAGGGAACTTCAAACAGTTCAACATCTTCTGTCATATGCTGGAGTCAGCCCTCACTCAGAGCAGTGAG
TCAGTCACTCTGGACCTGCTTACCTACACAGACCTGGAGTCCCTGCGGAACCACAAGTTGGGGGGCCGTCCAGGCCCTCT
GGCCCCCAGATCGGCCTAGTTCAACTCCAAGCGCTACCTAATCCTCATCTACTCAGTGGAGTTTGACAGGATTCACTACC
CGCTGCCCCTCCCGTACCAGGGCAAGCCAGACCCTGTGGTTCTGCAGGGCATCATCCACTCACTGAAGGAGGAACTGAGC
CGCCTGCAAGGGCTGGGCGGCCAGGATACTCGGGACACCCGGGAGACTGAGATCTGGCACCTGCGGGAGCAGGTGACGCG
CCTGGCATCAGAGAAGCGCGAGCTGGAGGTGCAGCCGGGCCGATCGCGCGAGGAAGCGCTGGCTGGGCGCGCGGCCCGCC
AGGAGGCCAAGGCATTGCGTGGGTTGGTGCGTGGGCTGGAGCTGGAGCTACTGCAGGAGCGCGTCCTTGGGCATAGGGTG
GCTGGCCGCCGAGGCTAGGACTGCCGCCGCCTGGCCAAGGAGCTCGAGGAGGCGAAGGCATCCGAGCGGAGCCTGCAAGC
CCAGCTGAAGACGCTGACCAGCGAGCTGGCCTTGTACAAGAGG
ORF - retro_cjac_1033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.81 % |
| Parental protein coverage: | 58.79 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDQPAGLQVDYVFRGVEHAVRVVVSGQVLELEVEDRMTADQWRGEFDAGFIEDLTHKTGNFKQFNIFCHM |
| M.Q.AGLQVDYVFRGVEHAV.VVV.GQVLEL.VEDRMT..QW.GEFDAGFIE.LTHKTGNFKQFNIFCHM | |
| Retrocopy | MGQLAGLQVDYVFRGVEHAVQVVVTGQVLELKVEDRMTVVQWGGEFDAGFIENLTHKTGNFKQFNIFCHM |
| Parental | LESALTQSSESVTLDLLTYTDLESLRNRKMGGRPGPLAPRSAQLNSKRYLILIYSVEFDRIHYPLPLPYQ |
| LESALTQSSESVTLDLLTYTDLESLRN.K.GGRPGPLAPRSA..NSKRYLILIYSVEFDRIHYPLPLPYQ | |
| Retrocopy | LESALTQSSESVTLDLLTYTDLESLRNHKLGGRPGPLAPRSA*FNSKRYLILIYSVEFDRIHYPLPLPYQ |
| Parental | GKPDPVVLQGIIRSLKEELGRLQGLGGQDTRDTRETEIWHLREQVSRLASEKRELEVQLGRSREEALAGR |
| GKPDPVVLQGII.SLKEEL.RLQGLGGQDTRDTRETEIWHLREQV.RLASEKRELEVQ.GRSREEALAGR | |
| Retrocopy | GKPDPVVLQGIIHSLKEELSRLQGLGGQDTRDTRETEIWHLREQVTRLASEKRELEVQPGRSREEALAGR |
| Parental | AARQEAEALRGLVRGLELELRQERGLGHRVAGRRGQDCRRLAKELEEAKASERSLRARLKTLTSELALYK |
| AARQEA.ALRGLVRGLELEL.QER.LGHRVAGRRG.DCRRLAKELEEAKASERSL.A.LKTLTSELALYK | |
| Retrocopy | AARQEAKALRGLVRGLELELLQERVLGHRVAGRRG*DCRRLAKELEEAKASERSLQAQLKTLTSELALYK |
| Parental | R |
| R | |
| Retrocopy | R |
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 | 1 .29 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .32 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .66 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .19 RPM |
| SRP051959_lung | 0 .03 RPM | 2 .90 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .60 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .57 RPM |
| SRP051959_spleen | 0 .00 RPM | 1 .81 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1033 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1033 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1033 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012104 | 1 retrocopy |
retro_cjac_1033 ,
|