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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaggcaatcattatgatttatggccctaacccatatggctccacttcttccttttcctttgcatgctgtaatcctttgttgcactgttatatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG

Basic information

species Zea mays
transcript GRMZM2G081144_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081144_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g08260.1 (Oryza sativa), 3'ss of exon 5
tgtaggcaatcattatgattta-tggccct-aacccatatg-gctccacttcttccttttcctttgcatgctgtaatcctttgttgcactgttatatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
 ||  ||| |    |  ||| | |  |||| ||   |  || | |     ||    ||||||||  |    | ||||   |||||   ||  | | | | |||||||||||||| ||||||||  |||||||||||||||
ggtgagcactatagacaattgagtaaccctcaagagacttgagatttggatcactgttttccttaac---ttataattagttgtttttcttctttctattcagGTTGAGATGATTCTTCAAGCATTGGAGTATGAAAAGG
















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|71766517|gb|DR964454.1|DR964454
EST:     ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGAGGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|31910399|gb|CD651404.1|CD651404
EST:     ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|30705910|gb|CD058965.1|CD058965
EST:     ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|50336894|gb|CO532020.1|CO532020
EST:     ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|30705290|gb|CD058734.1|CD058734
EST:     ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: ATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|27521943|gb|CA989049.1|CA989049
EST:     TTGGAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATCCTTCAAGCTCTGGAGTATGAAAAGG
genomic: TTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
EST: gi|29130952|gb|CB381656.1|CB381656
EST:     GAAGCGAAGGTTGTCAAAGATTTTGACAAG                         GTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
genomic: GAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG

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), 37 (downstream exon)
Score: 182

CACAAGAAATTCGTGAACTTTGGATGGAGTATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 284

CACAAGAAATTCGTGAACTTTGGATGGAGTATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG


Block sizes: 46 (upstream exon), 37 (downstream exon)
Score: 74

CACAAGAAATTCGTGAACTTTGGATGGAGTATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 180

CACAAGAAATTCGTGAACTTTGGATGGAGTATGAGGAGAATGCGTCTTTGGAAGCGAAGGTTGTCAAAGATTTTGACAAGgtacagtttc ... atatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttccttttcctttgcatgctgtaatcctttgttgcactgttatatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG
                                              tatttcc  CT-rich tract
                                         tgttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaggcaatcattatgatttatggccctaacccatatggctccacttcttccttttcctttgcatgctgtaatcctttgttgcactgttatatttccagGTTGAGATGATACTTCAAGCTCTGGAGTATGAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
tgtaggc
- - - - - - - - - - - - - - - - ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca