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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactttgactagccctgtttttagtattttatttcaactattgactataatacatgtgttcttctcag

Basic information

species Zea mays
transcript GRMZM2G079538_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 2
ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactttgactagccctgtttttagtatt--ttatttcaactattgactataatacat--gtgttcttctcag
|| ||||||||| | ||||||||| |||||| ||| | ||||| ||||||||||||||||| ||  || |||     || | || | | ||  || |||| |   ||| || |||||  |  ||  | || ||||
ACTCTAGGCCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgatt-gacatattctatattaattgttagttgtttctagctttggctctaatatgtaggtacttttttcag
















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|211233033|gb|FK998526.1|FK998526
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAR                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|78103875|gb|DV522298.1|DV522298
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211169881|gb|FL077610.1|FL077610
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148950981|gb|EC896624.2|EC896624
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|31355469|gb|CD439826.1|CD439826
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAGCTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211233035|gb|FK998528.1|FK998528
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAGCTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148978727|gb|EE026283.2|EE026283
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211321201|gb|FL380429.1|FL380429
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211233031|gb|FK998524.1|FK998524
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCG-AG
EST: gi|211169879|gb|FL077608.1|FL077608
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148958216|gb|EC904424.2|EC904424
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|31358640|gb|CD442997.1|CD442997
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAGCTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211325989|gb|FL407943.1|FL407943
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148991485|gb|EE033000.2|EE033000
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCC--G
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211233036|gb|FK998529.1|FK998529
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|149014456|gb|EE044070.2|EE044070
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|149003557|gb|EE038930.2|EE038930
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|67033243|gb|CO461992.1|CO461992
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148943959|gb|EC889039.2|EC889039
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211169872|gb|FL077601.1|FL077601
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|148931436|gb|EC874404.2|EC874404
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|78111553|gb|DV529950.1|DV529950
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|149081048|gb|EE170148.2|EE170148
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|149009740|gb|EE041651.2|EE041651
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|149015063|gb|EE044815.2|EE044815
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211169620|gb|FL396011.1|FL396011
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|31353408|gb|CD437765.1|CD437765
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAGCTTTCAG                         CTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
EST: gi|211233034|gb|FK998527.1|FK998527
EST:     CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG                         CTTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG
genomic: CCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTT-GGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG

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), 40 (downstream exon)
Score: 254

ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 485

ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 286

ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 442

ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactt ... ttcttctcagCTTTGGTTTCTGCTACATCTGAATGCTCAAATCTGCCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAGgttgttactttgactagccctgtttttagtattttatttcaactattgactataatacatgtgttcttctcag

- - - - - - - AAGGAG
- - - - - - - - - - - - - - - -  AGAAGC