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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgccatatcttggagcactactttgttcaccattggccaattaggtttgtgtcatattgacactaaggtgccaacattctctcccatgtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA

Basic information

species Zea mays
transcript GRMZM2G053764_T02
intron # 5
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|32859163|gb|CD998844.1|CD998844
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCAGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|12968800|gb|BG265836.1|BG265836
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|6022600|gb|AW067412.1|AW067412
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGGGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|5713918|gb|AI943903.1|AI943903
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|32859162|gb|CD998843.1|CD998843
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCAGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|60396538|gb|DN229407.1|DN229407
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|5649980|gb|AI920340.1|AI920340
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|1337735|gb|W49441.1|W49441
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|32859414|gb|CD999095.1|CD999095
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCAC
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCAC
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|5608383|gb|AI901960.1|AI901960
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|87156694|gb|DY401483.1|DY401483
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|211174889|gb|FL306344.1|FL306344
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCA
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCA
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCC
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCC
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
EST: gi|113551844|gb|DW724990.1|DW724990
EST:     GCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGG
genomic: GCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAA-Ggtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGG
EST: gi|211174894|gb|FL306349.1|FL306349
EST:     TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAG

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: 381

CCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1303

CCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1084

CCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 645

CCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGTCCTGTTTATGAACAGAAAGTGAAAGgtacagtggt ... gtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtttgtgtcatattgacactaaggtgccaacattctctcccatgtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA
            tattgac  putative branch site (score: 645)
                                  ttctctcccatgtttc  putative PPT
         tcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgccatatcttggagcactactttgttcaccattggccaattaggtttgtgtcatattgacactaaggtgccaacattctctcccatgtttctgcagAATATTGTGAGAAGTATGCCAAACCAGAGGACGCTGGTATCACTCCGGAAGACAAGTCCAGTGATGAAGAGCTTAGCGAGGAGGAAGACGACTCCGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA