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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagctttcaagcctgacgaaatctgcccaaccgtaatgtgtgctgaacggaaactgttttttttccttactgaaaacatgatctcttgcag

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 11
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|149046686|gb|EE048076.2|EE048076
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|60401221|gb|DN234028.1|DN234028
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|60336952|gb|DN203925.1|DN203925
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|148933118|gb|EC876753.2|EC876753
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|149035100|gb|EE155086.2|EE155086
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|60356145|gb|DN223118.1|DN223118
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|166651502|gb|EG153905.1|EG153905
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACC
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACC
EST: gi|76934720|gb|DV173991.1|DV173991
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|87152206|gb|DY396995.1|DY396995
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|30704808|gb|CD058607.1|CD058607
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|24770082|gb|CA405211.1|CA405211
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|60401592|gb|DN234399.1|DN234399
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|76933169|gb|DV173348.1|DV173348
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|37374628|gb|CF623690.1|CF623690
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|78109694|gb|DV528110.1|DV528110
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|71447792|gb|DR828842.1|DR828842
EST:     ACTACGGCAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|67012372|gb|CO441121.1|CO441121
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGATAGCATGATCTTATTATCGG                         GTTGATGTTCCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|4827733|gb|AI668425.1|AI668425
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|76280582|gb|DV020150.1|DV020150
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|78023793|gb|DV492180.1|DV492180
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|71447793|gb|DR828843.1|DR828843
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|148963078|gb|EE014035.2|EE014035
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATTTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|60345869|gb|DN212842.1|DN212842
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|76281418|gb|DV020986.1|DV020986
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|91051055|gb|EB161473.1|EB161473
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|22490578|gb|BU050501.1|BU050501
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|40336431|gb|CK370501.1|CK370501
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
EST: gi|19058545|gb|BM737212.1|BM737212
EST:     ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGG                         GTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG
genomic: ACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTG

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), 46 (downstream exon)
Score: 89

TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTGCTCCGGCGCATCAGTTTGTTGGCATGTTGATGGGGGTCGCGTGTTGTCA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 23

TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTGCTCCGGCGCATCAGTTTGTTGGCATGTTGATGGGGGTCGCGTGTTGTCA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 34

TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTGCTCCGGCGCATCAGTTTGTTGGCATGTTGATGGGGGTCGCGTGTTGTCA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 66

TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagcttt ... tctcttgcagGTTGATGTTTCGTTCAATCATGGAACCAGAGCAGAGCTAATATATGTCCTGCTCCGGCGCATCAGTTTGTTGGCATGTTGATGGGGGTCGCGTGTTGTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTTCAACCAGGACTACGGTAGCCATGTCGTTTGTTCAGAGCTAGCATGATCTTATTATCGGgtaaagctttcaagcctgacgaaatctgcccaaccgtaatgtgtgctgaacggaaactgttttttttccttactgaaaacatgatctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT