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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctacctgactgaccatttctttttcattgcccatcattcatcgtgatagttgatggttgaagtcttctggatacatacacgcgctggagtatgtatctgtaacgcctttctcccttgtgttgcgaccag

Basic information

species Zea mays
transcript GRMZM5G848603_T03
intron # 8
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|76924733|gb|DV170107.1|DV170107
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|71771831|gb|DR969768.1|DR969768
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|71421242|gb|DR805356.1|DR805356
EST:     AGCAACATCTTCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATTTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|211455215|gb|FL443682.1|FL443682
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|50331305|gb|CO526431.1|CO526431
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|71306517|gb|DR789416.1|DR789416
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|78110730|gb|DV529128.1|DV529128
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|149107875|gb|EE292236.2|EE292236
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|31353484|gb|CD437841.1|CD437841
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCG
EST: gi|76014004|gb|DT941174.1|DT941174
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
EST: gi|71315893|gb|DR794634.1|DR794634
EST:     AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG                         GGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG
genomic: AGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 40

AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctac ... ttgcgaccagGGTGCTCAAGAACATCTCGTCCAGCATCATCGCCCTTGTTACAGAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGGgtaggtctacctgactgaccatttctttttcattgcccatcattcatcgtgatagttgatggttgaagtcttctggatacatacacgcgctggagtatgtatctgtaacgcctttctcccttgtgttgcgaccag

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