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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcctgagccattctggtagctcttaatacacatcgtggtggctccaaactctactgaacaactgtcgttatctttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA

Basic information

species Zea mays
transcript GRMZM2G128491_T01
intron # 4
splice site 3'
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|32829824|gb|CD969502.1|CD969502
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|32828662|gb|CD968340.1|CD968340
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAGCA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|87157807|gb|DY402596.1|DY402596
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|76287576|gb|DV027144.1|DV027144
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78106237|gb|DV524655.1|DV524655
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|71307158|gb|DR789750.1|DR789750
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|148956639|gb|EC902493.2|EC902493
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|211435716|gb|FL461639.1|FL461639
EST:     AAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGMCAGCCCAGTGAAAMCA
genomic: AAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78114333|gb|DV532722.1|DV532722
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|12968693|gb|BG265639.1|BG265639
EST:     GATCGGACTATGGCAGCTCTGCTGCTCAGTCACCAATGAAAAATGCAAAC                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAACACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|71430885|gb|DR811935.1|DR811935
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|211018202|gb|FL215892.1|FL215892
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTT
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTT
EST: gi|71430884|gb|DR811934.1|DR811934
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78118764|gb|DV537148.1|DV537148
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|32829298|gb|CD968976.1|CD968976
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|22715254|gb|BU197664.1|BU197664
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|22819528|gb|BU499618.1|BU499618
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78083802|gb|DV512195.1|DV512195
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|76936903|gb|DV174954.1|DV174954
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|71327882|gb|DR800570.1|DR800570
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78083801|gb|DV512194.1|DV512194
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATACAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCGGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|32828948|gb|CD968626.1|CD968626
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|148956638|gb|EC902492.2|EC902492
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCGGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|211018194|gb|FL215884.1|FL215884
EST:     AAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: AAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
EST: gi|78118763|gb|DV537147.1|DV537147
EST:     GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAAT                         GTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA
genomic: GATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACA

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: 173

TCACGACATCTTTGCCGATCACGAAGATCCCAAGCCCAACAGGTCAAGGAGATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 115

TCACGACATCTTTGCCGATCACGAAGATCCCAAGCCCAACAGGTCAAGGAGATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 64

TCACGACATCTTTGCCGATCACGAAGATCCCAAGCCCAACAGGTCAAGGAGATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 329

TCACGACATCTTTGCCGATCACGAAGATCCCAAGCCCAACAGGTCAAGGAGATCAGACTATGGCAGCTCTGCTGCTCAGTCACCAGTGAAAAATGCAAATgtactgcctg ... ttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatcgtggtggctccaaactctactgaacaactgtcgttatctttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA
                                       ttatcttt  CT-rich tract
                                       ttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcctgagccattctggtagctcttaatacacatcgtggtggctccaaactctactgaacaactgtcgttatctttgttaacagGTGAGCTCCTTCTCGTTTGGAGAGGCCGACATTGACAGCACAGTGAAAACAGCAAAGAAGAAAGGGTCCAGCAACTTGTCTACTGATCTGAACGGCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA