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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatcttgttctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattag

Basic information

species Zea mays
transcript GRMZM2G095969_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095969_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G38780.1 (Glycine max), 5'ss of exon 7
GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatcttgttctcctatgcac-agaaattggc---atttaatctattcatttctgagtgatttattt--tgtattag------------------------------------------
|| |||||  |||| |||||||| ||||| |||||||| ||||| || || || ||||| || |||||||||||| || |||     |    |  |  ||||||  |    ||| | ||  ||  | | | | || ||| | |  | |||||                                           
GTGGTTGCAATTGGAGAATGTGGATTGGACTATGACAGGCTTCATTTTTGCCCAGCAGAGATTCAAAAGAAgtatgcagtctcacgattacctttattagaaatgtgtcctattaactccttttctcttttattgttttttgtaatatattaaaataatcaaccagtcatttgttttcttatctgtgaaatcaag

upper sequence: GRMZM2G095969_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT3G52390.2 (Arabidopsis thaliana), 5'ss of exon 7
GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgta--tacaatcttgt----tctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattag--
|| || ||  ||||||||||||| |||||||||||||| ||||| || ||  | |  ||||| || ||||||||  |   ||| |      | || | |  |||    ||  | | || |  |   || |     || ||| |||  |   |   
GTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAAgtaagtttgatcataaaaagtttcatgtttacattgtttt-cttctatttgaaatatcttcctatgttttctttgttgagaaag
















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|101392457|gb|EB818158.1|EB818158
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|88757501|gb|DY541642.1|DY541642
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|78179334|gb|DV549707.1|DV549707
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|71774366|gb|DR972244.1|DR972244
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATACGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|74242558|gb|DT650472.1|DT650472
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|7009462|gb|AW455727.1|AW455727
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|94477631|gb|EB706589.1|EB706589
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|71325561|gb|DR799471.1|DR799471
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|76936926|gb|DV174965.1|DV174965
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211484453|gb|FL145754.1|FL145754
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTTGAGAAACAATTTGAGTTGGCTGAAGCGGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|76021692|gb|DT948862.1|DT948862
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|78108903|gb|DV527320.1|DV527320
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT

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: 46 (upstream exon), 49 (downstream exon)
Score: 71

GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 47

GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG


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

GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 27

GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatcttgttctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA