RetrogeneDB ID: | retro_cjac_1900 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:36464124..36464898(-) | ||
| Located in intron of: | ENSCJAG00000016883 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NRM | ||
| Ensembl ID: | ENSCJAG00000019904 | ||
| Aliases: | None | ||
| Description: | nurim (nuclear envelope membrane protein) [Source:HGNC Symbol;Acc:8003] |
Retrocopy-Parental alignment summary:
>retro_cjac_1900
ATGGCCCCTGCACTGCTCCTGGTCCCTGCTGCCCTCGCCTCTTTCATCCTAGCCTTTGGCACTGGAGTGGAGTTTACGCA
CTTTACCTCCCTTCAGTCACTTCTTGGAGGGATCCCAGAGTCTGGTGGTCCCAATGCCTGACAGGGATGGCTGGCTGCCC
TGCAGGACCGCAGCATCCTTGCCCCCCTGGCATGGGATCTGGGGCTCCTGCTTCTATTTGTTGGGCAGCACAGCCTCATA
GCAGCTGAGAGAGTGAAACCATGGCCATCCCGGTACTTTGGGGTCCTTCAGAGGTCACTGTATGTGGCCTGCACTGCCCT
GGCCTTGCAGCTGGTGATGCGGTACTGGGAGCCTGTACCCAGAGGCCCCGTGTTGTGGGAGGCTCGAGCTGAGCCATGGG
CCACCTGGGTGCCCCTCCTCTGCTTTGTGCTCCATATCATCTCCTGGCTCCTCATCTTCAGCATCCTTCTCGTCTTTGAC
TACACTGAGCTCATGGGCCTCAAACAGGTGTACTACCATGTGCTGGGGCTGGGCGAGCCTCTGGCCCTGAAGTCTCCCCG
GGCTCTCAGTCTCTTCTCCCACCTGCGCCACCCAGTGTGTGTGGAGCTGCTGACAGTGCTGTGGGTGGTGCCTACGCTTG
GCACAGACCATCTCCTCCTTACCCTCTACCTGGGCCTGGCTCATAGGCTTGATCAGCAAGACCTCTGCTACCTCCGGGCC
CAGCTGCAAAGAAAACTCCACCTGCTCTCTCGACCCCAGGATGGGGAGGCAGAG
ORF - retro_cjac_1900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.98 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPALLLVPAALASFILAFGTGVEFVRFASLQPLLGGIPESVGPDARQGWLAALQDRSILAPLAWDLGLL |
| MAPALLLVPAALASFILAFGTGVEF..F.SLQ.LLGGIPES.GP.A.QGWLAALQDRSILAPLAWDLGLL | |
| Retrocopy | MAPALLLVPAALASFILAFGTGVEFTHFTSLQSLLGGIPESGGPNA*QGWLAALQDRSILAPLAWDLGLL |
| Parental | LLFVGQHSLMAAERVKAWTSRYFGVLQRSLYVACTALALQLVMRYWEPIPRGPVLWEARAEPWATWVPLL |
| LLFVGQHSL.AAERVK.W.SRYFGVLQRSLYVACTALALQLVMRYWEP.PRGPVLWEARAEPWATWVPLL | |
| Retrocopy | LLFVGQHSLIAAERVKPWPSRYFGVLQRSLYVACTALALQLVMRYWEPVPRGPVLWEARAEPWATWVPLL |
| Parental | CFVLHVISWLLIFSILLVFDYAELMGLKQVYYHVLGLGEPLALKSPRALRLFSHLRHPVCVELLTVLWVV |
| CFVLH.ISWLLIFSILLVFDY.ELMGLKQVYYHVLGLGEPLALKSPRAL.LFSHLRHPVCVELLTVLWVV | |
| Retrocopy | CFVLHIISWLLIFSILLVFDYTELMGLKQVYYHVLGLGEPLALKSPRALSLFSHLRHPVCVELLTVLWVV |
| Parental | PTLGTDRLLLALLLTLYLGLAHGLDQQDLRYLRAQLQRKLHLLSRPQDGEAE |
| PTLGTD.LLL....TLYLGLAH.LDQQDL.YLRAQLQRKLHLLSRPQDGEAE | |
| Retrocopy | PTLGTDHLLL----TLYLGLAHRLDQQDLCYLRAQLQRKLHLLSRPQDGEAE |
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 | 2 .13 RPM | 1 .24 RPM |
| SRP051959_heart | 1 .61 RPM | 2 .17 RPM |
| SRP051959_kidney | 2 .17 RPM | 1 .20 RPM |
| SRP051959_liver | 1 .04 RPM | 0 .80 RPM |
| SRP051959_lung | 2 .20 RPM | 3 .48 RPM |
| SRP051959_lymph_node | 4 .00 RPM | 2 .40 RPM |
| SRP051959_skeletal_muscle | 1 .55 RPM | 1 .35 RPM |
| SRP051959_spleen | 1 .87 RPM | 1 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1900 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1900 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1900 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 | ENSCJAG00000019904 | 1 retrocopy |
retro_cjac_1900 ,
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