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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttacattggatttgttttttttttctgttttactaaatctgcagaaattttattttggtcattgaaattttcatgtttattttaatttgacccc...

Basic information

species Zea mays
transcript GRMZM2G027756_T01
intron # 17
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|26558313|gb|CA830548.1|CA830548
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|37388207|gb|CF631310.1|CF631310
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|60338478|gb|DN205451.1|DN205451
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGTTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|21809667|gb|BQ667985.1|BQ667985
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|32931563|gb|CF036375.1|CF036375
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGTTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|76282536|gb|DV022104.1|DV022104
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|26557878|gb|CA830113.1|CA830113
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|26456119|gb|CA827702.1|CA827702
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|21987637|gb|BQ779165.1|BQ779165
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|32930056|gb|CF034868.1|CF034868
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGTTGTTCATGCCTTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC
EST: gi|20208212|gb|BQ134301.1|BQ134301
EST:     CTGTAGTTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCACTGCTGTTCATGCCTTCCTTGATTC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGC-CTGCTGTTCATGCCTTCCTTGATTC
EST: gi|33091466|gb|CF051460.1|CF051460
EST:     CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAG                         GCTACTGGTGACAAGTTTGATCGGCCTGTTGTTCATGCCCTCCTTGATTCC
genomic: CTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCC

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: 48 (upstream exon), 28 (downstream exon)
Score: 198

TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCCTTGATGGATTTAGAACGTGATATACCTGGATCATGCGAAGTACTGGTTG


Block sizes: 45 (upstream exon), 28 (downstream exon)
Score: 94

TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCCTTGATGGATTTAGAACGTGATATACCTGGATCATGCGAAGTACTGGTTG


Block sizes: 48 (upstream exon), 28 (downstream exon)
Score: 66

TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCCTTGATGGATTTAGAACGTGATATACCTGGATCATGCGAAGTACTGGTTG


Block sizes: 48 (upstream exon), 28 (downstream exon)
Score: 110

TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttac ... catgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCCTTGATGGATTTAGAACGTGATATACCTGGATCATGCGAAGTACTGGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCATTGCTACTCCCTTCCCTGAAAGAGgtaaagttacattggatttgttttttttttctgttttactaaatctgcagaaattttattttggtcattgaaattttcatgtttattttaatttgacccc

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