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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagcaattcaagttatttggtgacataccagtaacactggaacacagtttgtttttgtcaagtgctatcttaatttacacattatttttaatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT

Basic information

species Zea mays
transcript GRMZM5G832989_T01
intron # 10
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|67015040|gb|CO443789.1|CO443789
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|78544693|gb|DV622191.1|DV622191
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|31350085|gb|CD434442.1|CD434442
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|19769676|gb|BQ034397.1|BQ034397
EST:     ATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: ATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|60400346|gb|DN233153.1|DN233153
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|5670873|gb|AI932136.1|AI932136
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|32934733|gb|CF039545.1|CF039545
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACGGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|166649081|gb|EG056494.1|EG056494
EST:     CTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACGGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATC-AA
genomic: CTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|32934768|gb|CF039580.1|CF039580
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACGGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|9953633|gb|BE640216.1|BE640216
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|32934475|gb|CF039287.1|CF039287
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACGGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|60356638|gb|DN223611.1|DN223611
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|37376622|gb|CF624859.1|CF624859
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACGGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
EST: gi|78025368|gb|DV493755.1|DV493755
EST:     CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAG                         AACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA
genomic: CGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAA

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: 191

AGATAGCTGCTTTGGAGAAAAAATTTGCCGCGGTGTGCCTTGAACAAGAACGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT


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

AGATAGCTGCTTTGGAGAAAAAATTTGCCGCGGTGTGCCTTGAACAAGAACGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 52

AGATAGCTGCTTTGGAGAAAAAATTTGCCGCGGTGTGCCTTGAACAAGAACGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 46

AGATAGCTGCTTTGGAGAAAAAATTTGCCGCGGTGTGCCTTGAACAAGAACGGCTTGGTAATTTGAGAGGACCTGGAACTTCTCAGACTGTTTCGGGAAGgtatgccctt ... aatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttgtttttgtcaagtgctatcttaatttacacattatttttaatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT
                                         ttttaat  putative branch site (score: 46)
                     tatcttaatttacaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagcaattcaagttatttggtgacataccagtaacactggaacacagtttgtttttgtcaagtgctatcttaatttacacattatttttaatgctgcagAACTGCATCACGAGGTGGATTGACGCGCAACCTCCAATAGCATACATCTAACTTCAGGCAGGCATGGAATTCGTCCATAGGCTTCATTTCCATTGTATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - tttggtg
- - - - - - - - - - - - catacca
- - - - - - - - - - - - - - - - - -cactgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtgc