RetrogeneDB ID: | retro_mmus_2283 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:103644835..103646023(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000087119 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Atg4a | ||
| Ensembl ID: | ENSMUSG00000079418 | ||
| Aliases: | Atg4a, AI627006, AV169859, Apg4a, Atg4al, Autl2 | ||
| Description: | autophagy related 4A, cysteine peptidase [Source:MGI Symbol;Acc:MGI:2147903] |
Retrocopy-Parental alignment summary:
>retro_mmus_2283
ATGGAGTCAGTTATGTCCAAGTATGAAAACCAGATTCTTATTTTCCCTGACTACCTGGAAGAATTCCCGGATACAGATGA
GCTGGTATGGATTCTGGGGAAGCAGCACCCCTTTAAGACAGAAAAATCTAAGCTGTTGTCTGATATAAGTGCTCGCCTAT
GGTTTACATACAGAAGGAAATTTTCCCCGATTGGGGGAACAGGCCCTTCATCTGATGCTGGATGGGGATGTATGCTGCGT
TGTGGGCAGATGATGCTGGCTCAAGCCCTCATCTGCAGACACTTGGGAAGGGATTGGAACTGGGAGAGACAAAAAGAACA
ACCCAAAGAATACCAAAGGATACTGCAGTGTTTCCTAGATAGAAAAGACTGTTGCTATTCAATCCATCAGATGGCACAAA
TGGGTGTAGGAGAAGGGAAATCAATTGGCGAATGGTTTGGACCAAACACAGTTGCACAGGTGATAAAAAAACTCACTTTA
TTTGATGAATGGAATTCCTTGGCTGTTTATGTTTCCATGGATAACACAGTGGTCATTGAAGATATCAAGAAAATGTGCTG
TGTTCTTCCTGTGGGTGCTGCTGACCCAGCTGGTGATTTTCTGACTGTATCCAATCAGAGTAGAGACACCTCTGTCCCGT
GCTCAGCCTGGAAACCCCTGCTGCTCATTGTGCCCCTTCGCTTGGGCATAAACCAAATCAATCCTGTGTATGTTGAAGCA
TTCAAAGAGTGTTTTAAGATGCCACAGTCTTTAGGGGCTTTAGGAGGAAAGCCAAATAACGCCTATTATTTCATAGGATT
CTTAGGAGATGAGCTCATTTTTTTGGACCCTCACACAACCCAGACTTTTGTTGACATTGAAGAGAGTGGACTAGTAGACG
ACCAGACTTTTCATTGCCTGCAGTCTCCACAGCGGATGAGTATCCTGAACTTGGATCCTTCTGTGGCCTTGGGATTTTTC
TGCAAAGAAGAGAAAGACTTTGATAATTGGTGTAGCCTTGTTCAGAAGGAAATTCTAAAGGAGAATTTGAGGATGTTTGA
ATTGGTTCAGAAGCACCCATCACACTGGCCTCCCTTTGTACCTCCAGCCAAGCCAGAAGTGACAACCACAGGGGCAGAAT
TCATAGAGTCGACTGAACAACTGGAGGACTTTGAGCTGGAGGAAGATTTTGAAATTCTGAGTGTAGGC
ORF - retro_mmus_2283 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.24 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHPLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPS |
| MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHP.KTEKSKLLSDISARLWFTYRRKFSPIGGTGPS | |
| Retrocopy | MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHPFKTEKSKLLSDISARLWFTYRRKFSPIGGTGPS |
| Parental | SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK |
| SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK | |
| Retrocopy | SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK |
| Parental | SIGEWFGPNTVAQVIKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLTASNQSRDT |
| SIGEWFGPNTVAQVIKKL.LFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLT.SNQSRDT | |
| Retrocopy | SIGEWFGPNTVAQVIKKLTLFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLTVSNQSRDT |
| Parental | SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT |
| SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT | |
| Retrocopy | SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT |
| Parental | QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ |
| QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ | |
| Retrocopy | QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ |
| Parental | KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG |
| KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG | |
| Retrocopy | KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG |
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 .02 RPM | 3 .32 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 3 .08 RPM |
| SRP007412_heart | 0 .03 RPM | 6 .10 RPM |
| SRP007412_kidney | 0 .15 RPM | 7 .76 RPM |
| SRP007412_liver | 0 .14 RPM | 3 .80 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .78 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2283 was not detected
No EST(s) were mapped for retro_mmus_2283 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_90649 | 100 libraries | 106 libraries | 656 libraries | 177 libraries | 33 libraries |
The graphical summary, for retro_mmus_2283 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_2283 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2283 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gorilla gorilla | ENSGGOG00000002971 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000026280 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000079418 | 1 retrocopy |
retro_mmus_2283 ,
|
| Nomascus leucogenys | ENSNLEG00000014016 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020619 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000022170 | 1 retrocopy |