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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacccactcctttatcttaaagaaatgttcagtttgaagagggaatgaggggaattggcagaaaactgaagtcaattccatgccaaccccctcccaatccctgcacaactgaacaagggagtaaataatcttttccttccaggatattaacatttacacccaaatctgcag

Basic information

species Zea mays
transcript GRMZM2G156638_T02
intron # 14
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|16925759|gb|BM078827.1|BM078827
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|113703304|gb|EE680808.1|EE680808
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|33100101|gb|CF060061.1|CF060061
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|9961402|gb|BE644385.1|BE644385
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATT
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATT
EST: gi|16923090|gb|BM076082.1|BM076082
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|211523712|gb|FL481395.1|FL481395
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|14244490|gb|BG842508.2|BG842508
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|28986772|gb|CB351302.1|CB351302
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|14204013|gb|BG837690.1|BG837690
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|71758986|gb|DR956923.1|DR956923
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATTTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG
EST: gi|8102613|gb|AW927416.1|AW927416
EST:     TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGG                         GAGGAACAGGAGGGCACTCATTTACGACAAGTGGGTTATCTTCATCTCTTG
genomic: TGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTG

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: 109

TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTGCAAGAAAGGATTATGGGAGCATCTTTTAGTGTGTTGTGGACAGGAGGAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 159

TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTGCAAGAAAGGATTATGGGAGCATCTTTTAGTGTGTTGTGGACAGGAGGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 204

TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTGCAAGAAAGGATTATGGGAGCATCTTTTAGTGTGTTGTGGACAGGAGGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 83

TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacc ... aaatctgcagGAGGAACAGGAGGGCACTCATTTACGACAAGTGGGCTATCTTCATCTCTTGCAAGAAAGGATTATGGGAGCATCTTTTAGTGTGTTGTGGACAGGAGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAACCAGGCAACTTCCAGTCCGATGCGGCCAATGGGAAGCCATCACAGTGGGCAGCCTGCGTGGCCTAGTTTTGGCATGGGCGATGGAGTGCCCTGGGgtaacctacccactcctttatcttaaagaaatgttcagtttgaagagggaatgaggggaattggcagaaaactgaagtcaattccatgccaaccccctcccaatccctgcacaactgaacaagggagtaaataatcttttccttccaggatattaacatttacacccaaatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA