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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctactaattttggcgaccttctgagctgctgattgttctacctaacactgggtttccacattctgtcatgtgttctgcgcaatgtgcttatatccgatggtttttggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA

Basic information

species Zea mays
transcript GRMZM2G103430_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g14430.1 (Oryza sativa), 3'ss of exon 3
gtagctactaattttggcgaccttctgagctgctgattgttctacctaacactgggtttccacattctgtcatgtgttctgcgcaatgtgcttatatccgatggttt--ttggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA
                   ||||| | |||| ||| ||| ||  | ||     || |||     |||| ||| || |        ||||||||| ||  ||||||||  |   || || ||||||||||  |||||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||| || | ||||||||||| |  || |  ||| 
--------------gtattaccttgt-agct-ctg-ttggtcgccatagaggaggcttt----gttctatcacgtat-------gatgtgcttacattggatggtttggtctttggtgcagGGGAGGACACTGCGGTGCTCACTGTCGCAGGCAAAGCACAGGCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCC

upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 3
gtagctactaattttggcgaccttctgagctgctgattgttctacctaacactgggtttccacattctgtcatgtgttctgcgcaatgtgcttatatccgatggttt--ttggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA
                          |   || ||  | |      |  ||| | | ||| | |||   ||| || |         ||  ||||| |  |||||| |  |  ||| || ||||||||||  ||||||||||  |||| ||||||||||||||||| |||||||| ||||| ||||||||| |||| ||||| ||||| |  ||||  ||| 
--------------------------gtattg-tggctctctgggttgccacagaggttcta-attgcatcacgtat-------ggtgcacttatgttggatggtatggtccgtggtgcagGGGAGGACACTGCGGTGCTCATTGTCACAGGCAAAGCACAGGCTATTTGTTGGCAATGTACCCAAGGGGTTGAGTGAGGACGAGCTGAGAAACATAATCC
















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|211247169|gb|FL378129.1|FL378129
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
EST: gi|211280752|gb|FL403186.1|FL403186
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGTGCTCT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCT
EST: gi|28910015|gb|CB331214.1|CB331214
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
EST: gi|21809456|gb|BQ667774.1|BQ667774
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGT
EST: gi|211124642|gb|FL376727.1|FL376727
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAG                         GGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTYTGTT
genomic: AGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTT

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), 47 (downstream exon)
Score: 369

TAAGGACACAAAGGAGAACAAGGGGTTCGCCTTTGTCACCTTCATGGACAAGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TAAGGACACAAAGGAGAACAAGGGGTTCGCCTTTGTCACCTTCATGGACAAGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 215

TAAGGACACAAAGGAGAACAAGGGGTTCGCCTTTGTCACCTTCATGGACAAGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

TAAGGACACAAAGGAGAACAAGGGGTTCGCCTTTGTCACCTTCATGGACAAGGAGGCTGCGCAGCGCGCCATCGAGGATGTGCAAGACAGGGAGTTCAAGgtagctacta ... ggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtcatgtgttctgcgcaatgtgcttatatccgatggtttttggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA
                           ttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctactaattttggcgaccttctgagctgctgattgttctacctaacactgggtttccacattctgtcatgtgttctgcgcaatgtgcttatatccgatggtttttggtgctgtagGGGAGGACTTTGCGGTGCTCTCTGTCGCAGGCAAAGCACAGGCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT