RetrogeneDB ID: | retro_mmus_212 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:24333202..24333898(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000055826 | |
| Aliases: | Tescl, 1700008P20Rik | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tesc | ||
| Ensembl ID: | ENSMUSG00000029359 | ||
| Aliases: | Tesc, 1010001A17Rik, 2410011K10Rik, TE-1 | ||
| Description: | tescalcin [Source:MGI Symbol;Acc:MGI:1930803] |
Retrocopy-Parental alignment summary:
>retro_mmus_212
ATGGGCGCCTCCCTTTCGTCCAAGGAGGAGTGGGAGCGCGAGAGCAGGACCGACTTATGGTGGGCGCACATCCAGGAGGT
GTTGAACAAGTGCGACTTCAGCTGGGAGCAGATCAAGCAGCTGCACCAGAGGTTCAGGCTGCTGAGCGGGGACCAGCCCA
CCCTACAGCCAGAGAGCTTCGACAACATCCTGGACTTGGAGTTCAATCCGATCCGCTCCAGGATCGTCCGCGCCTTCTTC
GACAACCGGAACCTGGGCAAAGGGACCAGCGGTCTGGCGGAGGAGATCACCTTCCAGGACTTCCTGACCATCATCTCCTA
CTTCCGGCCGCTGCGGCCCAGTCTCAACAAAGAGGAGGCGGAGCAGAACCGCAAGGACAAGATGCGGTTCCTCTTCAACA
TGTACGACCAGGACGGCGATGGGATCATTACCCTGCAGGAGTACCGCCGGGTGGTGGAGAGCCTGCTGTCGGCGCACCCG
CAAGTGGAGAGAGACACTGTGCGCTCCGTCGCCAATGCCATCGCCCAGGGCGCCTTGAAGGAGGCGGCCAGGGCGTCGGA
CCAGCCGCTGATGGCGGGCCAGCAGTATGAGGGCATCACCTTCGAGGACTTCGTCAAGACCTGGAAGAGCCTCGAATTGG
AGGTGAAGATGCAAGTCAGCTTCCTGAATCTAGAAGCCACGGTCTTATGCCAGTGA
ORF - retro_mmus_212 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.52 % |
| Parental protein coverage: | 94.86 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VRELEGKTGFSSDQIEQLHRRFKQLSGDQPTIRKENFNNVPDLELNPIRSKIVRAFFDNRNLRKGSSGLA |
| ..E...K..FS..QI.QLH.RF..LSGDQPT...E.F.N..DLE.NPIRS.IVRAFFDNRNL.KG.SGLA | |
| Retrocopy | IQEVLNKCDFSWEQIKQLHQRFRLLSGDQPTLQPESFDNILDLEFNPIRSRIVRAFFDNRNLGKGTSGLA |
| Parental | DEINFEDFLTIMSYFRPIDTTLGEEQVELSRKEKLKFLFHMYDSDSDGRITLEEYRNVVEELLSGNPHIE |
| .EI.F.DFLTI.SYFRP....L..E..E..RK.K..FLF.MYD.D.DG.ITL.EYR.VVE.LLS..P..E | |
| Retrocopy | EEITFQDFLTIISYFRPLRPSLNKEEAEQNRKDKMRFLFNMYDQDGDGIITLQEYRRVVESLLSAHPQVE |
| Parental | KESARSIAD----GAMMEAASVCVGQMEPDQVYEGITFEDFLKIWQGIDIETKMHIRFLNMETIALC |
| ....RS.A.....GA..EAA..........Q.YEGITFEDF.K.W.....E.KM...FLN.E...LC | |
| Retrocopy | RDTVRSVANAIAQGALKEAARASDQPLMAGQQYEGITFEDFVKTWKSLELEVKMQVSFLNLEATVLC |
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 .00 RPM | 25 .75 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 34 .09 RPM |
| SRP007412_heart | 0 .03 RPM | 86 .67 RPM |
| SRP007412_kidney | 0 .02 RPM | 34 .90 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .44 RPM |
| SRP007412_testis | 55 .66 RPM | 1 .28 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_212 was not detected
No EST(s) were mapped for retro_mmus_212 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_132259 | 1062 libraries | 4 libraries | 2 libraries | 1 library | 3 libraries |
| TSS #2 | TSS_132260 | 1067 libraries | 2 libraries | 0 libraries | 1 library | 2 libraries |
| TSS #3 | TSS_132261 | 1063 libraries | 6 libraries | 1 library | 0 libraries | 2 libraries |
The graphical summary, for retro_mmus_212 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_212 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_212 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Rattus norvegicus | retro_rnor_244 |
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000012517 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000009300 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000009509 | 1 retrocopy | |
| Equus caballus | ENSECAG00000011177 | 1 retrocopy | |
| Felis catus | ENSFCAG00000002633 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000001775 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000029359 | 1 retrocopy |
retro_mmus_212 ,
|
| Rattus norvegicus | ENSRNOG00000001128 | 1 retrocopy |