RetrogeneDB ID: | retro_mmus_1783 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:63543753..63545135(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eef1a1 | ||
| Ensembl ID: | ENSMUSG00000037742 | ||
| Aliases: | None | ||
| Description: | eukaryotic translation elongation factor 1 alpha 1 [Source:MGI Symbol;Acc:MGI:1096881] |
Retrocopy-Parental alignment summary:
>retro_mmus_1783
ATGGGAAAGGAAAAGACTCACATCAACATCGTCGTAATCGGACACGTAGATTCCGGCAAGTCTACCACAACCGGCCACCT
GATCTACAAATGCGGTGGAATCGACAAGTGAACCATTGAAAAGTTTGAGAAGGAGGCTGCTGAGATGGTAAATGGCTCCT
TCAAGTACGCCTGGGTCTTAGACAAACTGAAAGCTGAGCGTGAGTGTGGTATCACTACTGACATCTCCCTGTGGAAACTC
GAGACCAGCGAATACTATGTGACCATCATTGATGCCCCAGGACACAGAGACTTCATCAAAAACATGATTACAGGCACATC
CCAGGCTGACCTTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTCATACCTCCAAGAACGGGCAGACCC
TCGAGCATGCTCTTCTGGCTTACACCATGGGTGTGAAACAGCTGATTGTTAGTGTCAACAAAATGGATTCCACCGAGCCA
CCATACAGTCAGAAGAGATACGAGGAAATCATTAAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCTGACAC
AGTAGCATTTGTGCCATTTTCTGGTTGAAATAGTGACAACATGCTGGAGCCAAGTGCTAATATGCCTTGGTTCAAGGGAT
GGAAAGTCACCTGCAAAGATGGCAGCGCCAGTGGCACCATACTGCTGGAAGCTTTGGATTGTATCCTACCACAAACTCGT
CCAACTGACAAGCCTCTGTGACTGCCCCTCCAGGATGTCTATAAAATTAGAGGCATTGGCACTGTCCCTGTGGGCCAAGT
GGAGACTGGTGTTCTCAAACCTGGCATGGTGGTTACCTTTGCTCCAGTCAATGTAACAACTGAAGTCAAGTCTGTTGAAA
TGCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTAAAGAATGTGTCGGTCAAAGATGTT
AGACGAGGCAATGTTGCTGGTGACAGCAAAAACGACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCT
GAACCATCCAGGCCAAATCAGTGCTGGCTATGCTCCTGTTCTGGATTGTCACACAGCCCACATAGCATGCAAGTTTGCTG
AGCTTAAAGAAAAGATCGATCGTCGTTCTGGTAAGAAGCTGGAAGATGGCCCCAAATTCCTGAAGTCTGGTGATGCTGCC
ATTGTTGATATGGTCCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCTGACCATCCTCCACTTGGTCGTTTTGCTTGTGA
CACGAGGCAGACAGTTGCTGTGGGTGTCATCAAAGCTGTGGACAAGAGGCTGCTGGAGCTGGCAAAGTTACCAAGTCTGC
CCAGAAAGCTCAGAAGGCTAAA
ORF - retro_mmus_1783 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.74 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG |
| MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDK.TIEKFEKEAAEM..GSFKYAWVLDKLKAERE.G | |
| Retrocopy | MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDK*TIEKFEKEAAEMVNGSFKYAWVLDKLKAERECG |
| Parental | ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA |
| IT.DISLWK.ETS.YYVTIIDAPGHRDFIKNMITGTSQAD.AVLIVAAGVGEFEA..SKNGQT.EHALLA | |
| Retrocopy | ITTDISLWKLETSEYYVTIIDAPGHRDFIKNMITGTSQADLAVLIVAAGVGEFEAHTSKNGQTLEHALLA |
| Parental | YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW |
| YT.GVKQLIV.VNKMDSTEPPYSQKRYEEI.KEVSTYIKKIGYNPDTVAFVP.SG.N.DNMLEPSANMPW | |
| Retrocopy | YTMGVKQLIVSVNKMDSTEPPYSQKRYEEIIKEVSTYIKKIGYNPDTVAFVPFSG*NSDNMLEPSANMPW |
| Parental | FKGWKVTRKDGSASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF |
| FKGWKVT.KDGSASGT.LLEALDCILP.TRPTDKPL.LPLQDVYKI.GIGTVPVG.VETGVLKPGMVVTF | |
| Retrocopy | FKGWKVTCKDGSASGTILLEALDCILPQTRPTDKPL*LPLQDVYKIRGIGTVPVGQVETGVLKPGMVVTF |
| Parental | APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP |
| APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP | |
| Retrocopy | APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP |
| Parental | GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP |
| GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSD.PP | |
| Retrocopy | GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDHPP |
| Parental | LGRFAVRDMRQTVAVGVIKAVDKK-AAGAGKVTKSAQKAQKAK |
| LGRFA..D.RQTVAVGVIKAVDK..AAGAGKVTKSAQKAQKAK | |
| Retrocopy | LGRFAC-DTRQTVAVGVIKAVDKR<AAGAGKVTKSAQKAQKAK |
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 .26 RPM | 938 .67 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 652 .71 RPM |
| SRP007412_heart | 0 .16 RPM | 465 .27 RPM |
| SRP007412_kidney | 1 .31 RPM | 1781 .75 RPM |
| SRP007412_liver | 0 .85 RPM | 2430 .48 RPM |
| SRP007412_testis | 0 .41 RPM | 1060 .92 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1783 was not detected
No EST(s) were mapped for retro_mmus_1783 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_60601 | 40 libraries | 27 libraries | 540 libraries | 361 libraries | 104 libraries |
The graphical summary, for retro_mmus_1783 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_1783 was not experimentally validated.