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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgcgttggcttcctgtgcttttcaatcaccaaaactgccaaggcctagttgttatggtgctaatggaggcgatttgaggttggtggagatcca...

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 2
CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgcgttggcttcctgtgcttttcaatcaccaaaactgccaaggccta--gttgttatggtgctaatggaggcga-tttgaggttggtggagatcca
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CCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCAAGGTCGGCGTCGTGCTCTCCGGCGGTCAGGCGCCCGGCGGCCACAATGTCATCTGCGGCATCTTCGgtgagtgcgc-tagtgttctcgagctgtttgttaaccctgtttacccaaggctatggaggatcagttctctgtacaagcgaatttgaagctcgtggt--ttcg
















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|29167975|gb|CB411235.1|CB411235
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211362770|gb|FL362322.1|FL362322
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211458486|gb|FL255599.1|FL255599
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|149083748|gb|EE173108.2|EE173108
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|148953762|gb|EC899129.2|EC899129
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211336175|gb|FL255583.1|FL255583
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTA
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTA
EST: gi|211336169|gb|FL255577.1|FL255577
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAATGCATCACCTTGTATGGATTTAANGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211458479|gb|FL255592.1|FL255592
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211458477|gb|FL255590.1|FL255590
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211334013|gb|FL255572.1|FL255572
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211336171|gb|FL255579.1|FL255579
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|5268364|gb|AI770328.1|AI770328
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211462254|gb|FL324872.1|FL324872
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211179440|gb|FL364368.1|FL364368
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211540563|gb|FL329390.1|FL329390
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGNCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211336168|gb|FL255576.1|FL255576
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|149083929|gb|EE173306.2|EE173306
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211187935|gb|FL314087.1|FL314087
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211336179|gb|FL255587.1|FL255587
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTAT
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTAT
EST: gi|211458484|gb|FL255597.1|FL255597
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211523118|gb|FL350158.1|FL350158
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211414893|gb|FL345683.1|FL345683
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211458480|gb|FL255593.1|FL255593
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211336170|gb|FL255578.1|FL255578
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211458364|gb|FL364597.1|FL364597
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|149103124|gb|EE288493.2|EE288493
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|20803238|gb|BQ294288.1|BQ294288
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|31354738|gb|CD439095.1|CD439095
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|148963458|gb|EE014477.2|EE014477
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|211334009|gb|FL255568.1|FL255568
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
EST: gi|149105648|gb|EE291200.2|EE291200
EST:     CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTG                         ACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG
genomic: CTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAG

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), 45 (downstream exon)
Score: 288

CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 231

CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 248

CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 369

CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgc ... gttggatcagACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGTTGTGCTCTCCGGTGGACAGGCGCCGGGCGGCCACAATGTCATCTGCGGCATCTTTGgtgagtatgcgttggcttcctgtgcttttcaatcaccaaaactgccaaggcctagttgttatggtgctaatggaggcgatttgaggttggtggagatcca

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