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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 6
gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG
||     ||  | | || |||  |   || ||| |   |     ||     |    | |||   ||| |||| ||  |||||  | |  ||   ||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||| | || |||||
gttccttctttagagatatcttgt---ttgttcctacttcttgcatgtatatcagttttttccctgaactaatatgttgtatccgttctttc--ttgcagGATCTAACCTCTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCAAGTGACCACAATGGAAACTTAACAAACCG

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 5
--gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttg--gtactttgt-ttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG
  ||| |   ||| ||   ||   |  || |     |      |  |||  | |||||  | ||||  |    |       ||||||  ||| ||| | ||| ||| || || ||| | ||||||||||| |||||  ||||||||||||||||||| || ||| | ||||| || |  || |||||||  || ||||| || ||
gtgtcctt-ttgctaatgccttc-caaagatacatgta-----caaattttggttttagatcttgtcaaatctattactcctatttgatgtattttctgttgcagGTTCGAATCTTCTCATAGACAATGAAGGTAATCTGAAGCTTGCTGATTTTGGACTGGCACGGTCATTTTCTAACGAGCACAATGCAAATCTTACAAATCG

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG
||  || ||  | |||  | |  ||    ||  |||  || ||| ||   |  | | | |  | | ||||    | || ||||||          |  ||| ||||| ||| | |||||||||||||| || ||||||||||| ||||||||||||||  | ||||| || | |||||||||||| || ||||| || ||
gttataacta-agacaagttttttg----ttatttgattttcttttttattaatgaggctaagctaagctg---ttctatatttg----------tacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------gtcttagctgcaa-acatctctgctgagt-----------ttttcttgtctt---ccttattcggtttt--tatgttttgttgagctaacatactg--tatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG-
               | | ||||| |  |  | ||   ||| |           |  | |||| ||   | |  ||  | | |   | ||  | |    |  || |   |  | | || ||  |  |||  ||| || || ||| | || |||||  | || |  |||||||||||||||||||| |||||||| || || || | |||||| |||||  | |  ||| ||   
gtaagttgtacggtttttcagctgaaccagctttccattgattaggaataacagtccttttgtattaatcttggtttagatctatcaagtcatatcttacctacttgtggattttctgatatctctttttcagGTTCAAATCTTCTTATCGACAACAATGGAATTTTGAAGCTTGCTGATTTTGGGCTTGCAAGGTCGTTTTCTAATGATCAGAATGGTCAACC-ACTGACAAA

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|71766382|gb|DR964319.1|DR964319
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|78078029|gb|DV506444.1|DV506444
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GGATCTAACCTTTTGATAGACAATGAGGGTA
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagG-ATCTAACCTTTTGATAGACAATGAGGGTA
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTT
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTT
EST: gi|149107723|gb|EE189597.2|EE189597
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|71430764|gb|DR811814.1|DR811814
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|149099519|gb|EE185557.2|EE185557
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAAACAATGA
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGA
EST: gi|211438449|gb|FL012011.1|FL012011
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|32844191|gb|CD983872.1|CD983872
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148969561|gb|EE020392.2|EE020392
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACATTGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|211325352|gb|FL255515.1|FL255515
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148954879|gb|EC900358.2|EC900358
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|32845306|gb|CD984987.1|CD984987
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|149087325|gb|EE176860.2|EE176860
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|148955711|gb|EC901398.2|EC901398
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
EST: gi|149106097|gb|EE291761.2|EE291761
EST:     AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAG                         GATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG
genomic: AGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTG

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: 283

TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 150

TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 140

TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAAGTTCTGCATCGAGATATCAAAGgtcttagctg ... ttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG
                     agctaac  putative branch site (score: 152)
                                           ctttgttt  putative PPT
     tttttatgttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA