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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattcagtttaccttggtatcatgctactataagtcgatgagtcagattgtcatataggaccgttgttttttctgctagcataaaggctacgtttatcttgtcttgtgtcagtactaattcattgatctttgtcgtcttggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG

Basic information

species Zea mays
transcript GRMZM2G121262_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 8
gtgaattcagtttaccttggtatcatgc-tactataagtcgatgagtcagattgtcata--taggaccgttgttttttct--gctagcataaaggctacg-tttatc------ttgtcttgtgtcagtactaattcattgatctttgtcgtcttggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
|| ||| || ||| | |||||  ||       | | ||   ||||||||   | | ||   | |    |||  |||| ||  |||||||||||  ||| | ||||||      ||| | ||        || || ||  ||  | |    ||  | || |  |||| || | ||||||||||||||||||||| || ||||||||||| |||| |
gtaaatccaattttctttggtgccacatgctttttcagggaatgagtcaatatataatcgttggatttgtttattttactatgctagcataaaatctatgatttatcatgtatttgccatgctctcaatctcatccaaagacatcttctttccggtaccaatagGCGCCATGTGAAGCAGAAGCAGAATGTGCTGCACTTTGCATAAATGATATG
















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|88749646|gb|DY533787.1|DY533787
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|28568845|gb|CB280720.1|CB280720
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGAT
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGAT
EST: gi|148983038|gb|EE028944.2|EE028944
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|26558947|gb|CA831182.1|CA831182
EST:     ACGAAGATTGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|30087247|gb|CB885455.1|CB885455
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAA
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAA
EST: gi|50328745|gb|CO523871.1|CO523871
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|148945123|gb|EC890320.2|EC890320
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|78117503|gb|DV535890.1|DV535890
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|5566733|gb|AI881599.1|AI881599
EST:     ACGAAGATTGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAA
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAA
EST: gi|148985935|gb|EE029848.2|EE029848
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|89763728|gb|DY690807.1|DY690807
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|22473079|gb|BU037559.1|BU037559
EST:     ACGAAGATTGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|31405508|gb|CD484240.1|CD484240
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|18661475|gb|BM501417.1|BM501417
EST:     ACGAAGATTGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|87156101|gb|DY400890.1|DY400890
EST:     ACGAAGATTGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|71444731|gb|DR825781.1|DR825781
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|74235361|gb|DT643275.1|DT643275
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|9952839|gb|BE639422.1|BE639422
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAAC
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAAC
EST: gi|93014006|gb|EB639526.1|EB639526
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|76018920|gb|DT946090.1|DT946090
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|32907157|gb|CF011970.1|CF011970
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|91054792|gb|EB165210.1|EB165210
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
EST: gi|60349759|gb|DN216732.1|DN216732
EST:     ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG                         GCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
genomic: ACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG

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), 49 (downstream exon)
Score: 434

GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAGgtgaattcag ... ggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttgtcttgtgtcagtactaattcattgatctttgtcgtcttggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG
                     taattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattcagtttaccttggtatcatgctactataagtcgatgagtcagattgtcatataggaccgttgttttttctgctagcataaaggctacgtttatcttgtcttgtgtcagtactaattcattgatctttgtcgtcttggacaaccagGCACCTTCTGAAGCAGAAGCAGAATGTGCAGCCCTTTGCATAAACGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC