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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctggggaggaacagaactagttttttttttcccgttactgactacagtttcctttgaaaggtgattaggtaatgtgcctgatcaacatatctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC

Basic information

species Zea mays
transcript GRMZM2G173354_T02
intron # 3
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|211534671|gb|FL445689.1|FL445689
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGCGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|148986479|gb|EE030223.2|EE030223
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTTTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|94475660|gb|EB704618.1|EB704618
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|71306414|gb|DR789352.1|DR789352
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|211097823|gb|FL296747.1|FL296747
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|101390441|gb|EB817155.1|EB817155
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|30306849|gb|CD001522.1|CD001522
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|33100086|gb|CF060046.1|CF060046
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAC                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|5761988|gb|AI967036.1|AI967036
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|71762381|gb|DR960318.1|DR960318
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|78090335|gb|DV518709.1|DV518709
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|86467750|gb|DY234120.1|DY234120
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|6022043|gb|AW066986.1|AW066986
EST:     CGTGTGCCAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCCCG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|78078858|gb|DV507270.1|DV507270
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTTTACTGTTACCTGGTGAGGATGAGTTTGTTTTCGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|26557637|gb|CA829872.1|CA829872
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|76010764|gb|DT937934.1|DT937934
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|95107853|gb|EB740082.1|EB740082
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|60340433|gb|DN207406.1|DN207406
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|71427864|gb|DR808914.1|DR808914
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|5740558|gb|AI948248.1|AI948248
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|67023051|gb|CO451800.1|CO451800
EST:     CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG
EST: gi|211097821|gb|FL296745.1|FL296745
EST:     TGTGACAGGGTTGTTTCTGATGTGAGCGGAGGNAGGGGTTANTTGGAGAG                         TATCCTCTACTGTTACCTGGCGAGGATGAGTTTGTCTACGAGAGTTGCAC
genomic: TGTGACAGGGTTGTTTCTGATGTGAGCGGAGG-AGGGGTTA-TTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCAC
EST: gi|76911327|gb|DV164233.1|DV164233
EST:     CGTGTGACAGGGTTGTTTTTGATGTGAGCGGAGGAGGGGTTATTGGAGAG                         TATCCTTTACTGTTACCTGGTGAGGATGAGTTTGTTTACGAGAGTTGCACG
genomic: CGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACG

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: 161

CGTGTACTATTCTTCCTGCCAGCTTTGCTCCCGCCACTGGACCATCAGATCGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CGTGTACTATTCTTCCTGCCAGCTTTGCTCCCGCCACTGGACCATCAGATCGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

CGTGTACTATTCTTCCTGCCAGCTTTGCTCCCGCCACTGGACCATCAGATCGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

CGTGTACTATTCTTCCTGCCAGCTTTGCTCCCGCCACTGGACCATCAGATCGTGTGACAGGGTTGTTTCTGATGTGAGCGGAGGAGGGGTTATTGGAGAGgtatcctggg ... tctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttcctttgaaaggtgattaggtaatgtgcctgatcaacatatctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC
                               gcctgat  putative branch site (score: 171)
        tttgaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctggggaggaacagaactagttttttttttcccgttactgactacagtttcctttgaaaggtgattaggtaatgtgcctgatcaacatatctcgtgcagTATCCTCTACTGTTACCTGGTGAGGATGAGTTTGTCTACGAGAGTTGCACGCCACTGCCCCAAGTACCAGGATCTGTGGAGGGCTCTTTTTCGTTTGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG