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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttccacgacttgcatgagcattgctgtattctgttgacatcgtaattttgcattcccaaactttaagaacagaaaatgctgcaagatatctttc...

Basic information

species Zea mays
transcript GRMZM2G014788_T01
intron # 25
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|211519911|gb|FL453783.1|FL453783
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|33092001|gb|CF051995.1|CF051995
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|211361549|gb|FL423686.1|FL423686
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32797514|gb|CD949750.1|CD949750
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCNCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|211041954|gb|FL378891.1|FL378891
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|60357426|gb|DN224399.1|DN224399
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32928505|gb|CF033317.1|CF033317
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|33091614|gb|CF051608.1|CF051608
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32848978|gb|CD988659.1|CD988659
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACCGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32942753|gb|CF047572.1|CF047572
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32908270|gb|CF013083.1|CF013083
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32933415|gb|CF038227.1|CF038227
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32908269|gb|CF013082.1|CF013082
EST:     CCATGTTGGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: CCATGTTGG-TCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|60399625|gb|DN232435.1|DN232435
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|67041526|gb|CO467781.1|CO467781
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCTTCTAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|211516406|gb|FL409520.1|FL409520
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|211413951|gb|FL082391.1|FL082391
EST:     TAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|211441921|gb|FL415411.1|FL415411
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32797592|gb|CD949828.1|CD949828
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|37383469|gb|CF628751.1|CF628751
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|6056869|gb|AW091274.1|AW091274
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|6020513|gb|AW065441.1|AW065441
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|60346132|gb|DN213105.1|DN213105
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|32932418|gb|CF037230.1|CF037230
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
EST: gi|5819266|gb|AI987472.1|AI987472
EST:     TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAG                         GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT
genomic: TCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTT

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), 47 (downstream exon)
Score: 204

TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 183

TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttcc ... tatgatgcagGAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGTTTGAATCGGAGTTAGTCGAAGTAGATCTGGAAAAGGATCCCCAAATCCATGTTGGTCCCCTCAAATATAAAACTGAGGAGCGTCATCAAAAGCAGgtaactttccacgacttgcatgagcattgctgtattctgttgacatcgtaattttgcattcccaaactttaagaacagaaaatgctgcaagatatctttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagaaaa