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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatatttatcacggtatgttagataatgtagtttttcttcctttacctatgtcaatgatcaaaatatgaattgattgatatgacatgcatttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG

Basic information

species Zea mays
transcript GRMZM2G124091_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 2
atatatttatcacggtatgttagataatgtagtttttcttcctttacctatgtcaatgatcaaaata-tgaattgattgatatgaca-tgcatttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
  |  |||| | |  |     || |  || |   ||  ||  || |  ||| |||   ||   | || ||| || ||  ||    || |   ||  |  |||||||||||||||||||||||||||||||| ||||||||||
-aaactttaactcaattaagcagctcgtgcatgcttgattagttcat-tatttcacctatttcattaatgatttaatcaattcatcagtatgttgtatgcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGGATAATCCTAG
















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|211283832|gb|FL366650.1|FL366650
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|89253024|gb|DY624810.1|DY624810
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|101399938|gb|EB821816.1|EB821816
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211477983|gb|FL231678.1|FL231678
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGATCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGC
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGC
EST: gi|211239068|gb|FL308505.1|FL308505
EST:     TGGCGATCGC-TTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         -TTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211359478|gb|FL332719.1|FL332719
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAGGAAT
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAGGAAT
EST: gi|149000975|gb|EE038215.2|EE038215
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211477979|gb|FL231674.1|FL231674
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGATCTAAGGATCCTAACCGGCAG                         -TTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211477985|gb|FL231680.1|FL231680
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGATCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGC
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGC
EST: gi|211500675|gb|FL332351.1|FL332351
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211125807|gb|FL321198.1|FL321198
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGACAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
EST: gi|211477978|gb|FL231673.1|FL231673
EST:     TGGCGATCGCCTTCCTTTCGGCTGAGCGATCTAAGGATCCTAACCGGCAG                         GTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAAATCCTAGG
genomic: TGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAA-TCCTAGG

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), 40 (downstream exon)
Score: 24

ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 7

ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 1

ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG


Block sizes: 43 (upstream exon), 39 (downstream exon)
Score: 7

ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaaca ... tttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctatgtcaatgatcaaaatatgaattgattgatatgacatgcatttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG
                            gattgat  putative branch site (score: 7)
                                             tttcactc  putative PPT
                aaaatatgaattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatatttatcacggtatgttagataatgtagtttttcttcctttacctatgtcaatgatcaaaatatgaattgattgatatgacatgcatttcactcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGAATAATCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca