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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattcatctgtttgggaaaaatacaatgcagtgcatcatttgttggtctggctattgacaaatgccttgtctctttttttttggctgtgtaatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 15
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|6851547|gb|AW352557.1|AW352557
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|28984456|gb|BQ539072.2|BQ539072
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|60395851|gb|DN228721.1|DN228721
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089695|gb|FL030414.1|FL030414
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCC-TGTT
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTT
EST: gi|211089690|gb|FL030409.1|FL030409
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTG
EST: gi|148948655|gb|EC898569.2|EC898569
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|71439289|gb|DR820339.1|DR820339
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|71760087|gb|DR958024.1|DR958024
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211507045|gb|FL413323.1|FL413323
EST:     ATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: ATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|67010801|gb|CO439550.1|CO439550
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089693|gb|FL030412.1|FL030412
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089692|gb|FL030411.1|FL030411
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATA
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATA
EST: gi|86467956|gb|DY234326.1|DY234326
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089696|gb|FL030415.1|FL030415
EST:     GTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAAWCATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGA
genomic: GTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAA-CATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGA
EST: gi|211092150|gb|FL030416.1|FL030416
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|166621297|gb|EG158029.1|EG158029
EST:     GGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: GGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG

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), 48 (downstream exon)
Score: 182

CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtctggctattgacaaatgccttgtctctttttttttggctgtgtaatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC
        tattgac  putative branch site (score: 199)
                           tcttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattcatctgtttgggaaaaatacaatgcagtgcatcatttgttggtctggctattgacaaatgccttgtctctttttttttggctgtgtaatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAGATCGACTGGGTGAACACGTACCACTCAGACTGCCGGAAGATCTTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
ccattca
- - - -tctgttt
- - - - - - - - -aaaaata
- - - - - - - - - - - - caatgca
- - - - - - - - - - - - - - - -gtgcatc
- - - - - - - - - - - - - - - - - - - - -tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - -gctattg