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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctcttttatcattctttttactgtcaaatgaatgccacggtcatacaataataaattgatttgtaataaaaattttcttaaaaagttctatagt...

Basic information

species Zea mays
transcript GRMZM2G178618_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 17
AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctcttttatcattctttttactgtcaaatgaatgccacggtcatacaata-ataaattgatttgtaataaaaattttcttaaaaagttctatagt-------
||| |  ||||| ||||| |||||||||||||| |  ||||| ||  ||||||||||||| |||||||| ||| ||||||||||||||||||| || ||||| |||| ||||      |  |||  || |  ||||||| | | |  |   || |   |||  |  | |   || | | |||| ||      ||||  |||       
AGAAAGCGAGCGGGTTGATGAGTATGGGCTTGGCGCCAGGGAAAGCCTGGCTGAGGCTGTGAGTGCTGTCATAGGCATCCTTGGCATGCAGCCCTGCGAGgtcagtcactttc-----taatttatctattgaatgaatacgaagtcctgccagtttgtaaccttttataccatgatagtttttttttt---ttctgaagttaatttt

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 17
AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctcttttatcattctttttactgtcaaa-tgaatgccacggtcatacaataataaattgatttgtaataaaaattttcttaaaaagttctatagt-
 ||   |||||| || || |||||||| |||||    || |||||||||||||| ||||||| | ||||||| | | | |||||| || ||||||||||||| ||    |  | ||| |   |    ||  ||| |   |     | ||||    || | || |  | | |   |    ||   |  ||| |||  | |   
TGATTTTGAGCGTGTGGATGAGTATGGTCTTGGTCCTAGAGAGAGTTTGGCTGAAGCTGTAAATACTGTTATCAACCTACTTGGCTTGGAGCCTTGTGAGgtaagctgatgatgtcaattgctgctttgataaactctcttttgagatcattt--tatttaacttgtatattgcacgtgttgcgtacaaaggttgcacaaag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 17
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 16
AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctcttttatcattctttt------tactgtcaaatgaatgccacggtcatacaataataaattgatttgtaa-taaaaattttcttaaaaagttc-tatagt--------------------------
|||   |||||| || ||||| ||||| |||||   ||| ||||||||||  || |||||||  ||||| ||     | |||||||||||| |||||||||||||||||||  |   || | |       |||||  |  |||  || |   | ||    | ||||| |  ||| | | || |       ||     |||| |  | |                          
AGAAGATGAGCGTGTAGACGAATATGGCCTTGGCCAAAGAGAGAGTTTGGGAGAAGCTGTAAAGGCTGTCATGGATCTTCTTGGCATGCAGACTTGTGAGgttagtctcttccacttttttctcatactctactgagacttgagggctaaaattat-tgttgataaagtcttttttgagtatatgaccatttgttgtgttcctgaaattgaaactgacactggataaataacag

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|32867952|gb|CF007634.1|CF007634
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|50337422|gb|CO532548.1|CO532548
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTTTTT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|74235980|gb|DT643894.1|DT643894
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTTTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|40334153|gb|CK368223.1|CK368223
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|211418623|gb|FK952669.1|FK952669
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|32867953|gb|CF007635.1|CF007635
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|71773316|gb|DR971224.1|DR971224
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|211418624|gb|FK952670.1|FK952670
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|7162448|gb|AW520070.1|AW520070
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGT
EST: gi|44901278|gb|CK827823.1|CK827823
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|50337423|gb|CO532549.1|CO532549
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|32944665|gb|CF049484.1|CF049484
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|71773315|gb|DR971223.1|DR971223
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTTTGCTTTTT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
EST: gi|211418626|gb|FK952672.1|FK952672
EST:     CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAG                         GGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT
genomic: CTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 396

AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCTGGTGTGTTTATTGGCAACGTGAAAGTCTTGGTGAGACTGTCATTTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCTGGTGTGTTTATTGGCAACGTGAAAGTCTTGGTGAGACTGTCATTTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCTGGTGTGTTTATTGGCAACGTGAAAGTCTTGGTGAGACTGTCATTTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 535

AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctct ... tggcttgtagGGAACTGACGTGGTCCCAAGCAATTCAAGGTCGCACACTTGTCTGCTCTCTGGTGTGTTTATTGGCAACGTGAAAGTCTTGGTGAGACTGTCATTTGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGACTGAGCGAGTTGACGAGTATGGGCTTGGAGTAAGGGAGAGTTTGGCTGAGGCTGTAAGTGCTGTTATAAGCATCCTTGGCATGCAGCCTTGTGAGgttagtctcttttatcattctttttactgtcaaatgaatgccacggtcatacaataataaattgatttgtaataaaaattttcttaaaaagttctatagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaaa