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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgactgagatgttttaatgaatgtggatcttggttaccgtatatctgccatgccaatatctttatatgctttgtggaactgtgatgtgctactga...

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 6
GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtga-ctgagatgttt-taatg--aatgtg-gatcttggttaccgtatatctgccatgc-caatatctttatatgctttgtggaactgtgatgt-gctactga
||||||||||| |||||||||||||||||||| ||  |||||||||||||| |||||||||||||| |  || ||    || ||  ||| ||  || || |||  | | |  ||   |||| |  |   || || |  ||    | |||     || ||||    
GTCAGACCTGTGGCTGAAGAAGAAATGTTCAAAGTTTTACGAACTGGCAAGAGAAAAAgtaagtgaacctaggtgccaatagtgtaaatctgtaatattagttgacatttggcttgtatgctcggtgcattcatgtattt----gtacttcctcgtagctag---
















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|8366902|gb|BE049910.1|BE049910
EST:     GTTGCTNGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: GTTGCT-GAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|78109120|gb|DV527537.1|DV527537
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|37398604|gb|CF636617.1|CF636617
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|71440545|gb|DR821595.1|DR821595
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60347312|gb|DN214285.1|DN214285
EST:     TGTTGTTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|50332540|gb|CO527666.1|CO527666
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|149079698|gb|EE168699.2|EE168699
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|211296298|gb|FL480002.1|FL480002
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|45847152|gb|CN071095.1|CN071095
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|211523708|gb|FL481391.1|FL481391
EST:     CTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: CTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60354693|gb|DN221666.1|DN221666
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|15053622|gb|BI359167.1|BI359167
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|78109119|gb|DV527536.1|DV527536
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|5739867|gb|AI947557.1|AI947557
EST:     GGCAAGCGAAAAC                         CCAACCAGTGGAAGAGAATGGTTNCCAAAGCCNCTTTTGTTGGAGCTGGAT
genomic: GGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|148933462|gb|EC877158.2|EC877158
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|17930472|gb|BM267432.1|BM267432
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|15053623|gb|BI359168.1|BI359168
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|45847376|gb|CN071319.1|CN071319
EST:     GCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCCAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: GCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60350420|gb|DN217393.1|DN217393
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|211487760|gb|FL392997.1|FL392997
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60340980|gb|DN207953.1|DN207953
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|50332541|gb|CO527667.1|CO527667
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|22545768|gb|BU098142.1|BU098142
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|31359359|gb|CD443716.1|CD443716
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGGGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAG
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAG
EST: gi|211464730|gb|FL207496.1|FL207496
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|15313826|gb|BI478973.1|BI478973
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCANGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTNGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|76917038|gb|DV166648.1|DV166648
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|22819549|gb|BU499639.1|BU499639
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT

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), 48 (downstream exon)
Score: 116

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


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

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgactgagatgttttaatgaatgtggatcttggttaccgtatatctgccatgccaatatctttatatgctttgtggaactgtgatgtgctactga

- - - - - -  CTGAAG
- - - - - - - TGAAGA
- - - - - - - - AAGAAG
- - - - - - - - -  AAGAAA