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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacgagccccgtccgccgtcaatgtttctttccattgattgcgtcggtgacccatttctgtcatcatctacttataatgaattgcag

Basic information

species Zea mays
transcript GRMZM2G140201_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140201_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g54300.1 (Oryza sativa), 5'ss of exon 3
CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacgagccccgtccgccgtcaatgtttctttccattgattgcgtcggtgac--ccatttctgtcatca-tctacttataatgaattgcag---------------------------
|||||| ||| ||||||||||||||||||| |||||||||||||||||||| |||||||||||| | |||||| | || || || || ||||| ||||||||  |  ||  | |   |  ||      ||    | || | | |      | | |||  | |||  ||   | | |||    |||||    |  |                            
CTTGACGGGGTTGGAGTACAGGGACGACCCTACCATCCTCGCGTGGGAGCTCATGAACGAGCCCAGATGCACCTCCGATCCATCTGGTGACACTCTGCAGgtgagtcact-gtcatatgggcgacatgtgccattgtcaaattaccttaaccgcgacttcaattcttgatgtgaatctggcaataatttggttgatcggtgtttggtgtctttgggtgtgcag
















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|71320023|gb|DR796776.1|DR796776
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|26559897|gb|CA832132.1|CA832132
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCAGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGGCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|76013121|gb|DT940291.1|DT940291
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCC
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCC
EST: gi|76010886|gb|DT938056.1|DT938056
EST:     TGATGAACGAGCCCCGCTGCATCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACCAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|78080285|gb|DV508697.1|DV508697
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGGAG-AGATGTCGGCGT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGG-AGGAGATGTCGGCGT
EST: gi|91055737|gb|EB166155.1|EB166155
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCTATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|76925541|gb|DV170475.1|DV170475
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGGATGGAG-AGATGTCGGCGTACGTCAA
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGG-ATGGAGGAGATGTCGGCGTACGTCAA
EST: gi|22819005|gb|BU499095.1|BU499095
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCAGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGGCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|89764483|gb|DY691272.1|DY691272
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|149112156|gb|EE191269.2|EE191269
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGA
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGA
EST: gi|78083938|gb|DV512331.1|DV512331
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|71444052|gb|DR825102.1|DR825102
EST:     GATGAACGAGCCCCGCTGCACCACGGACCCCCTC-GGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCCGCGTACGTCAA
genomic: GATGAACGAGCCCCGCTGCACCACGGACCCC-TCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAA
EST: gi|71438164|gb|DR819214.1|DR819214
EST:     TGATGAACGAGCCTCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCAT
EST: gi|76289545|gb|DV029113.1|DV029113
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|91872768|gb|EB402725.1|EB402725
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|148951355|gb|EC897071.2|EC897071
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTTCG-CGTACGTCAAGTC
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGT-CGGCGTACGTCAAGTC
EST: gi|148964465|gb|EC905820.2|EC905820
EST:     GATGAACGAGCCCCGCTGCACCACGGACCCCCTC-GGCGACACGCTGCAG                         CGCTGGATGGA
genomic: GATGAACGAGCCCCGCTGCACCACGGACCCC-TCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGA
EST: gi|87155942|gb|DY400731.1|DY400731
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCAGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGGCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCAT
EST: gi|71421768|gb|DR805561.1|DR805561
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAA                         CGCTGGATGGAGGAGATGT
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGT
EST: gi|76014710|gb|DT941880.1|DT941880
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCGGGCGACACGCTGCAG                         CGCTGGATGGGAG-AGATGTCGGCGTACGTCAAG
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGG-AGGAGATGTCGGCGTACGTCAAG
EST: gi|71765538|gb|DR963475.1|DR963475
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTC
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTC
EST: gi|148943315|gb|EC888373.2|EC888373
EST:     TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCCGCGACACGCTGCAG                         CGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCC
genomic: TGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCC

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: 55

CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCATCTGCTCACCGTCGGCACCGAGGGGTTCTACGGGCCGACGAGCCCCCAGG


Block sizes: 43 (upstream exon), 39 (downstream exon)
Score: 14

CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCATCTGCTCACCGTCGGCACCGAGGGGTTCTACGGGCCGACGAGCCCCCAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 27

CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCATCTGCTCACCGTCGGCACCGAGGGGTTCTACGGGCCGACGAGCCCCCAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 56

CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacg ... tgaattgcagCGCTGGATGGAGGAGATGTCGGCGTACGTCAAGTCCATCGACAAGAAGCATCTGCTCACCGTCGGCACCGAGGGGTTCTACGGGCCGACGAGCCCCCAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGACAGGGGTGGAGTACAGGGACGACCCCACCATCCTCGCGTGGGAGCTGATGAACGAGCCCCGCTGCACCACGGACCCCTCCGGCGACACGCTGCAGgttggcgacgagccccgtccgccgtcaatgtttctttccattgattgcgtcggtgacccatttctgtcatcatctacttataatgaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG