RetrogeneDB ID: | retro_mmus_1834 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:43280797..43281694(+) | ||
| Located in intron of: | ENSMUSG00000074852 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000047509 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lztfl1 | ||
| Ensembl ID: | ENSMUSG00000025245 | ||
| Aliases: | Lztfl1, 5530402H04Rik, 6130400H19Rik, AI414725, AW048545 | ||
| Description: | leucine zipper transcription factor-like 1 [Source:MGI Symbol;Acc:MGI:1934860] |
Retrocopy-Parental alignment summary:
>retro_mmus_1834
ATGGCAGAGTTGGGCCTAAATGAGCACCATCAAAATGAGGTCATTAATTACATGCATTTTGCTCGTTCAAAAAGAGGCTT
GAGACTTAAAACGGTAGATTCTTGCTTTCAGGACCTCAAAGACAGCAGGCTGGTGGAGGAGACTTTCACCATTGATGAGG
TTTCAGAAGTCCTAAATGGGCTGCAGGCTGTGGTACACAGTGAGGTGGAGTCTGAGCTCATCAATACAGCTTACACCAAT
GTCCTGCTCCTACGGCAGCTGTTCTCCCAAGCTGAGAAGTGGTATCTAAAGCTACAGACAGACATCTCTGAACTTGAAAA
CAGAGAATTATTAGAACAAGTTGCTGAATTTGAAAAGGCAGAATTTGTATCTTCAAGTAAAAAGCCCATCATAGATATCA
CAAAGCCTAAGCTTGTTCCGATTAATGAAGGTGGAACTACAGAGCTCCTAAACAAGGAAATTTTAAGACTTCAACAAGAG
AATGAAAAACTAAAGTCAAGGCTGAAGACCATTGAAATACAGGCTGTAAATGCTCTGGATGAGAAGTCAAAATTGGAAGG
AGTACTTCAAGATTTACAGCTCAATCAAGAAAACCAACAGGATTTTCTAAAGGCCCAAGACTTGGATGACTTGGAAAATA
CAGTTGCAACTCTTAGGAGTGAATTTCAGAAGACACTTAATGACAAGACAGAAAGCCAAAAATCTTTGGAGGAGAACCTA
GCAGCAGCCAAACATGACCTCCTCAGAGTACAGGAGCAGCTGAGCATGGCTGAAAAGGAGTTAGAGAAGAAATTTCAACA
AACAGCAGCTTATCGAAACATGAAAGAGATTCTCACCAAAAAGAATGATCAAATCAAAGACCTATGGAAAAGACTGGCAA
AATATGAATCTGAAGAT
ORF - retro_mmus_1834 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.99 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAELGLNEHHQNEVINYMRFARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE |
| MAELGLNEHHQNEVINYM.FARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE | |
| Retrocopy | MAELGLNEHHQNEVINYMHFARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE |
| Parental | SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP |
| SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP | |
| Retrocopy | SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP |
| Parental | INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLERVLQDLQLDQENQQDLLKAQDLDD |
| INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLE.VLQDLQL.QENQQD.LKAQDLDD | |
| Retrocopy | INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLEGVLQDLQLNQENQQDFLKAQDLDD |
| Parental | LENTVATLRSEFQKTLNDKTENQKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK |
| LENTVATLRSEFQKTLNDKTE.QKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK | |
| Retrocopy | LENTVATLRSEFQKTLNDKTESQKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK |
| Parental | KNDQIKDLRKRLAKYESED |
| KNDQIKDL.KRLAKYESED | |
| Retrocopy | KNDQIKDLWKRLAKYESED |
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 .05 RPM | 36 .42 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 20 .49 RPM |
| SRP007412_heart | 0 .03 RPM | 9 .65 RPM |
| SRP007412_kidney | 0 .06 RPM | 14 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .05 RPM |
| SRP007412_testis | 0 .32 RPM | 38 .10 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1834 was not detected
No EST(s) were mapped for retro_mmus_1834 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_65044 | 225 libraries | 253 libraries | 526 libraries | 51 libraries | 17 libraries |
The graphical summary, for retro_mmus_1834 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_1834 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1834 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000003899 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000013761 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000010237 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025245 | 3 retrocopies |
retro_mmus_1834 , retro_mmus_3266, retro_mmus_3276,
|
| Procavia capensis | ENSPCAG00000009783 | 1 retrocopy |