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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagctggttctcccactctcttactacttccgatccagctccagctcttccctttctaaaggtcttaggtagtgtttggttccggagtatgg...

Basic information

species Zea mays
transcript GRMZM2G162672_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 13
TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagctgg-ttctcccactctcttactacttccgatccagctccagctcttcc---ctttctaaa--ggtcttaggtagtgtttggtt-ccggagtatgg------------------------
||||| |||||||| |||||||||||||||||||| |||||||| |||||| ||||| | | | |||| | | ||  | |   |||||   ||   ||     || ||   |  |  |||  ||    |   |  |    ||   | ||  |  |                        
TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagcagtagaaactggagacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcag

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 14
-TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgt-----gcttcagctggttctcccactctcttactacttccgatc--cagctccagctcttccctttctaaaggtctt--aggtagtgtt----tggttccggagtatgg-----------------------------------
 ||| |||| |||||  ||||||||||||| |||||||| ||||||||||| |      ||| |  |     ||  |   |   |  |      |    ||     |||  |  | | |  | |||  |   || |     |    || ||   |||||                                      
GTTCAAGTATTTCCTCCAGGACCCTGTGAAATATGATGTTAAATATCAggtattaactacttaaatttagcttctaagcataacaagatggagaagtggcaaaatgagcaatgtcatattcataggaataggagatgacaatggcatgtttatagagtaaattattctaaactaattgaacattctcttgttttgca

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA16G19390.1 (Glycine max), 5'ss of exon 6
TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagct---ggtt---ctcccactctcttactacttccgatccagct---ccagctcttccctttc--taaaggtcttag-gtagtgtttggttccggagta--tgg----------------
||| |||| ||||  |||||||||||||| |||||||| |||||||||||     |   |      ||   || | |  |    |  | |   ||    ||      |||  | |||      |  |  ||||     |||   |  |||   | ||  ||                 
TTCAAGTATTTCCGCAAGGACCCTGTGAAATATGATGTTAAATATCAGgtacatattgaccttaaatttagcttctaagcataaaaaaatggagaagtggccaaatgagcaatgccccagaagtggacatctttttagagtaaattattctaaactaattgaacactcgtgtttgcag

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 14
TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagctggttctcccactctcttactacttccgatccagctccagctcttccctttctaaaggtcttaggtagtgtt-tggttccggagtatgg---------------------------------
||| |||| ||||| |||||||||||||| |||||||| |||||||||||     |   |   |      |   ||| |  |   |  |         ||        |    || |  ||  |  | ||   |  ||   |||||                                    
TTCAAGTATTTCCTCAAGGACCCTGTGAAATATGATGTTAAATATCAGgtacatattgacct-taaatttagcttctaagcataacaaaatggaga--agtggccaaatgagcaatgccctatgacaatgacatctttttagagtaaattattctaaactaattgaacactcgtgtttgcag

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|211036110|gb|FL230102.1|FL230102
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|71759623|gb|DR957560.1|DR957560
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATAT---                         -C-AGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|211433564|gb|FL478685.1|FL478685
EST:     CCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: CCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAN                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|71314948|gb|DR794088.1|DR794088
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|71324982|gb|DR799184.1|DR799184
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACACCCATTTTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|149110076|gb|EE293890.2|EE293890
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|71763867|gb|DR961804.1|DR961804
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|32931186|gb|CF035998.1|CF035998
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCGCAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA
EST: gi|148929759|gb|EE285358.2|EE285358
EST:     TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG                         GCAAGCGCACAACCATTTTTTGTACTGGGCCTACTGGTGACAGCACTGGCA
genomic: TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCA

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: 48 (upstream exon), 44 (downstream exon)
Score: 134

TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCAACCAGCCATTAATGAAGGCAAACTTAAACAGAACGAGCAACCGTTCTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 458

TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCAACCAGCCATTAATGAAGGCAAACTTAAACAGAACGAGCAACCGTTCTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 132

TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCAACCAGCCATTAATGAAGGCAAACTTAAACAGAACGAGCAACCGTTCTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 139

TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttca ... ttgctgatagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCAACCAGCCATTAATGAAGGCAAACTTAAACAGAACGAGCAACCGTTCTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagctggttctcccactctcttactacttccgatccagctccagctcttccctttctaaaggtcttaggtagtgtttggttccggagtatgg

- - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcccac