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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA

Basic information

species Zea mays
transcript GRMZM2G046587_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
------gacctttctatagaatataatataatatagttct-tgtaaactagttctgtcccaagg--ctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
       | |     | |  | | || |||||    |||| |   || |  || ||  | || |   ||| ||||| ||         ||  |  ||  |    |  |||| ||||||||||| ||||| ||||| || ||||||||||||||||||| ||| |||| || |||||||| |||  |||| || || |||||||||||||
agtcagtagcccaacacaagaaagaa-ataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacac--------atgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA

upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 6
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatc--ttatttaatcgttgttcaacatcacta--gGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
    ||    |    |  || ||   ||| |||   |||  |    |      ||| |  ||||     |    ||||||  |   |    ||     |||  ||| ||||  ||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||| |||||||  || || || || ||||| |||   || |
---tttcacttgtctttcaacattgcataattcgaataatttgtcaccacttaaagtccaaatttggagaaaaattatttt-tttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACTGACATCAATGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatt-taatcgttgttcaacatcacta--gGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
    ||    | |  |  || ||   ||| |||   |||  | ||     |  || |   || | | |      ||| || |   |    ||     |||  ||| ||||  ||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||| ||||||| ||| || || || ||||| |||   || |
---tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
     |   | | | | | | |    ||  | | | ||    |  | |  ||  ||   |||  |  | |||       | | |  |   | |     |||| |||||||| || ||||| || ||||| ||||||||||| || || |||||||||||||  |||||||  || || || || || || ||    || |
----gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatc-------accttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

upper sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 5
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattctt-gcatcttatttaatcgttgttcaacatcact---agGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
    | |||||| | |  |||   |  |  || || |  |  |  | |||  |||| |   |||    |  |  |    |   | |   |||   |  |   |||| || || ||||| || || |||||||| ||||||||||||||||| ||||| |||||||  |||||||  ||  | || || |||||||||   ||||
--agtctctatatatttaaattagacgtgttttttcttgatca--tatgtttcaagacaccattgaaagtgtgattaccaggtgatacacaaatccttttgcagGGTGAAAAGGATGACAAAATAATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19351061|gb|BM895593.1|BM895593
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGCAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATT
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCG-AGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATT
EST: gi|32849179|gb|CD988860.1|CD988860
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTTGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32924525|gb|CF029337.1|CF029337
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|18168735|gb|BM338575.1|BM338575
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|76016905|gb|DT944075.1|DT944075
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGGGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|60348368|gb|DN215341.1|DN215341
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|149099848|gb|EE185900.2|EE185900
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|74244614|gb|DT652528.1|DT652528
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13126527|gb|BG317097.1|BG317097
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGTAATAGTATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAA
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAG-AA-AG-ATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAA
EST: gi|60337363|gb|DN204336.1|DN204336
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32924252|gb|CF029064.1|CF029064
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|16919746|gb|BM074334.1|BM074334
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|16377933|gb|BI992193.1|BI992193
EST:     TTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: TTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32831285|gb|CD970963.1|CD970963
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13126526|gb|BG317096.1|BG317096
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 80

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 35

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtcccaaggctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA
                             atttaat  putative branch site (score: 128)
                        atcttatttaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA