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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTGTCCATGTCGTGCTCAAGGGGCTGGTGTTCCCAAACGGCGTGCAGATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaatactatctgacgatgctcatgattctaccgtatccatagtcatgaacacaaaccacacgaatctggccttgaccag

Basic information

species Zea mays
transcript GRMZM2G307906_T01
intron # 3
splice site 5'
intron type U2

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|149029397|gb|EE286196.2|EE286196
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACNACAAACTGCAG                         GATAATGAGGTACT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACT
EST: gi|148948291|gb|EC893808.2|EC893808
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|149069891|gb|EE158287.2|EE158287
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|116823121|gb|EC866629.1|EC866629
EST:     TTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GAT-ATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: TTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148939885|gb|EC884597.2|EC884597
EST:     CCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTTTT
genomic: CCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148960914|gb|EE011604.2|EE011604
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|149106557|gb|EE188449.2|EE188449
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148934313|gb|EC878339.2|EC878339
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|110958103|gb|EE178155.1|EE178155
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|18660011|gb|BM500639.1|BM500639
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGAGCGAG-TAGAG-TGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148928902|gb|EC873905.2|EC873905
EST:     CGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: CGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|211358965|gb|FL314618.1|FL314618
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         AATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTANAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|211031208|gb|FL344488.1|FL344488
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         AATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTG
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTG
EST: gi|148948226|gb|EC893742.2|EC893742
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGG
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGG
EST: gi|148960144|gb|EE153394.2|EE153394
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|211359944|gb|FL353310.1|FL353310
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGAGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|149029327|gb|EE154705.2|EE154705
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148953527|gb|EE153036.2|EE153036
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
EST: gi|148950756|gb|EC896356.2|EC896356
EST:     ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAG                         GATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT
genomic: ATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTT

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 2 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 15 (downstream exon)
Score: 2

GCGGTGTCCATGTCGTGCTCAAGGGGCTGGTGTTCCCAAACGGCGTGCAGATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTTCGCGAACCTGCCGGGCTTCCCCGACAACGTGCGCTCCAACGGCAGGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1592

GCGGTGTCCATGTCGTGCTCAAGGGGCTGGTGTTCCCAAACGGCGTGCAGATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaa ... ccttgaccagGATAATGAGGTACTGGCTGGAAGGCCCAAGAGCGGGCGAGGTAGAGGTGTTCGCGAACCTGCCGGGCTTCCCCGACAACGTGCGCTCCAACGGCAGGGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGTGTCCATGTCGTGCTCAAGGGGCTGGTGTTCCCAAACGGCGTGCAGATCTCAGAGGACCATCAGTTTCTTCTCTTCTCCGAGACAACAAACTGCAGgtaacaaaaatactatctgacgatgctcatgattctaccgtatccatagtcatgaacacaaaccacacgaatctggccttgaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG