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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 3
-------------gtgcgctcttatct-----cccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
              |     || ||||      |  |  ||||| |    ||   |  | |||| |||||   || | ||| ||  |        ||||   | ||| | ||| || || |||||||| ||||||||||||||||||||| |||| || ||||| || ||||| |||||||| || || |||| |||||||||||||||||| 
gtctgtatagtctatatatactgatctagcagtctcttttgctgttgc-cgccatgtctcgcaagttgctcggaacactgacattgg--------aacgatct-gatgtgtagTGTGGTTGAGAGTGTTGGTGAAGGTGTGACCGAGTTCGAAGTGGGAGACCATGTGCTCACCGTCTTCATCGGAGAGTGCATGAGCTGCAAGCACTGCGTT
















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|71771533|gb|DR969470.1|DR969470
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|50322631|gb|CO517757.1|CO517757
EST:     GCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|29946549|gb|CB816205.1|CB816205
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|148957215|gb|EC903225.2|EC903225
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 104

GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 202

GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 226

GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 227

GCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
                                       cgccttc  CT-rich tract
           ttctaataatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC