RetrogeneDB ID: | retro_mmus_2611 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:137928292..137929017(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Zwint | ||
| Ensembl ID: | ENSMUSG00000019923 | ||
| Aliases: | Zwint, 2010007E07Rik, 2600001N01Rik, D10Ertd749e, Zwint-1 | ||
| Description: | ZW10 interactor [Source:MGI Symbol;Acc:MGI:1289227] |
Retrocopy-Parental alignment summary:
>retro_mmus_2611
AGACAAAACGCTGTTGCGACGAAAGAGGTTCTGGCTGAGGCAGCAGCCATTCTAGAACCTGTAGGCTTGCAGGAAGAAGC
AGAGCTGCCTGCCAAGATCATGGAGGAGTTCATGAGGAAGTCGCGGAAGAAAGACAAACTGCTTTGTAGCCAGCTTCAAG
TAGTGAACTTCTTACAGACTTCTCTGCCTCAGGAGGATACTGACCAGAATCCAGATGCTTTGGCTTCTGAAGATGCAAGT
CGGCAAAAGGCAACTGAAACTAAGGAGCAGTAAAAGGACATGAAGGCCACATACATGGATCACGTGGATGTCATAAAATG
GGCCCTGTTGGAGGCCTTACCCCAGGTTAAAGAGGCTCACAGGAATTACAAAGAGCTTCAGAAGGCTTTTGAGCAACTCG
AGGCTAAGAAGCGAGTCCTTGAGGAGAAACTTCAGCTGGCTCAGAAGCAGTGGGCGCTGCAACAGAAGCGTTTGCAGAAT
CTGACAAAGACGTCTGCAGAGGTCAAGAGGCGCCGCGGGAAGAGGGCTCTGGAGAAGCTTGACGGACCCCACCAGGAACT
GGAAACCTTGAAGCAGCAAGCGGGACAGGAACAGGGGAAGCTGCAGAGGAACCAGAGCTACCTCCAGCTGCTGTGTTCCC
TGCAGAATAAGCTGGTCATCTCTGAGGGCAAGGCTGAGGACAAAATGTCAAAGGGCGAGCCCTTACAGCCAAATCCAAAT
CTCCT
ORF - retro_mmus_2611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.18 % |
| Parental protein coverage: | 95.63 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KNNAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMRNSRKKDKLLCSQLQVVNFLQTFLAQEDTEQS |
| ..NAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMR.SRKKDKLLCSQLQVVNFLQT.L.QEDT.Q. | |
| Retrocopy | RQNAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMRKSRKKDKLLCSQLQVVNFLQTSLPQEDTDQN |
| Parental | PDALASEDASRQKATETKEQWKDMKATYMDHVDVIKCALSEALPQVKEAHRKYTELQKAFEQLEAKKRVL |
| PDALASEDASRQKATETKEQ.KDMKATYMDHVDVIK.AL.EALPQVKEAHR.Y.ELQKAFEQLEAKKRVL | |
| Retrocopy | PDALASEDASRQKATETKEQ*KDMKATYMDHVDVIKWALLEALPQVKEAHRNYKELQKAFEQLEAKKRVL |
| Parental | EEKLQLAQKQWVLQQKRLQNLTKISAEVKRRR-KRALEKLDGSHQELETLKQQAGQEQEKLQRNQSYLQL |
| EEKLQLAQKQW.LQQKRLQNLTK.SAEVKRRR.KRALEKLDG.HQELETLKQQAGQEQ.KLQRNQSYLQL | |
| Retrocopy | EEKLQLAQKQWALQQKRLQNLTKTSAEVKRRRGKRALEKLDGPHQELETLKQQAGQEQGKLQRNQSYLQL |
| Parental | LCSLQNKLVISEGKAEDK-DVKGRALTAKSKSP |
| LCSLQNKLVISEGKAEDK..VKGRALTAKSKSP | |
| Retrocopy | LCSLQNKLVISEGKAEDK<NVKGRALTAKSKSP |
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 |
|---|---|---|
| SRP007412_brain | 0 .30 RPM | 713 .71 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 405 .77 RPM |
| SRP007412_heart | 0 .09 RPM | 37 .51 RPM |
| SRP007412_kidney | 0 .13 RPM | 61 .54 RPM |
| SRP007412_liver | 0 .03 RPM | 42 .74 RPM |
| SRP007412_testis | 0 .00 RPM | 46 .61 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2611 was not detected
No EST(s) were mapped for retro_mmus_2611 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_111172 | 710 libraries | 310 libraries | 51 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_2611 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_2611 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2611 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000002655 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000007793 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000019923 | 3 retrocopies |
retro_mmus_1488, retro_mmus_2611 , retro_mmus_997,
|
| Rattus norvegicus | ENSRNOG00000048682 | 2 retrocopies | |
| Tarsius syrichta | ENSTSYG00000010283 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000002204 | 1 retrocopy |