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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtttcggcctaaccgaatttagttgttctattcaatctgtagatttctgacctcactcagctgtgccagatgcgactgtttggcttgttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC

Basic information

species Zea mays
transcript GRMZM2G332809_T01
intron # 11
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|166649728|gb|EG261609.1|EG261609
EST:     CTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: CTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|60399213|gb|DN232027.1|DN232027
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|29945154|gb|CB815496.1|CB815496
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|211191428|gb|FL472425.1|FL472425
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|5069895|gb|AI737860.1|AI737860
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|32839425|gb|CD979106.1|CD979106
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|94476039|gb|EB704997.1|EB704997
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|32836647|gb|CD976325.1|CD976325
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|32837676|gb|CD977354.1|CD977354
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|5069885|gb|AI737850.1|AI737850
EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|32945118|gb|CF049937.1|CF049937
EST:     GGAG-TTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
EST: gi|211060187|gb|FL170394.1|FL170394
EST:     GGAG-TTGCTTTCAGACCACCTTTACACACAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 107

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagtttcggcctaaccgaatttagttgttctattcaatctgtagatttctgacctcactcagctgtgccagatgcgactgtttggcttgttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC

- - - - - - - - - - - - - - - - - - - - - - - tttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt