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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttttgcaaagcccaaagttttgtttcacaagttatattttatcaatcattgttcccttatccttaagcatatatctttgaaagatgtttcaagtggtgatctaactaagtatttcctttctcattttttacatgtactgatttgttcatttcgttggtatttatatatatatatatatatatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG

Basic information

species Zea mays
transcript AC233895.1_FGT001
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233895.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g28280.1 (Oryza sativa), 3'ss of exon 5
gtaagtgtttttgcaaagcccaaagttttgtttcacaagttatattttatcaatcattgttcccttatccttaagcatatatctttgaaagatgtttcaagtggtgatctaactaagtatttcctttctcattttttacatgtactgatttgttcatttcgttggtatttatatatatatatatatatatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG
                                                                            |  || | |    |  | ||    |   |||  ||| | |||       | |     |||    |||| |    || | || | |   |||   || | | | |           | ||||| |||||||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||
----------------------------------------------------------------------------agctaacct--gtatgtcttctctgcaatgaattaattcagt-------tgcatgcctttggtttgtattagaatgctgatcttgccagtaacaatttttcttt-----------tgcagAACAAGGATGTCACCGAAGCGATTCAGAAAGTTGCTGCTGCTTATGACTGCAAAATTGTGGAAGGAGTTCTCAGCCATCAGCTGAAACAGTTTGTCATTG
















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|32932980|gb|CF037792.1|CF037792
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|31351014|gb|CD435371.1|CD435371
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|22549146|gb|BU101347.1|BU101347
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|32850813|gb|CD990494.1|CD990494
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|22542895|gb|BU093333.1|BU093333
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATT
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATT
EST: gi|84980121|gb|DW530470.1|DW530470
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|32931969|gb|CF036781.1|CF036781
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|87155627|gb|DY400416.1|DY400416
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|22819488|gb|BU499578.1|BU499578
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|87157252|gb|DY402041.1|DY402041
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|32838111|gb|CD977789.1|CD977789
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|32838243|gb|CD977921.1|CD977921
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|32850802|gb|CD990483.1|CD990483
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|26559653|gb|CA831888.1|CA831888
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|22473335|gb|BU037815.1|BU037815
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|111990961|gb|EE332393.1|EE332393
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|26559180|gb|CA831415.1|CA831415
EST:     CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: CCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
EST: gi|33092800|gb|CF052794.1|CF052794
EST:     GCGGCTTGTGAGACCTGGGAAGAAA                         AATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC
genomic: GCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGC

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: 436

AATTACAAATGGGCCTGTCACAGGAAGGGCTGGTGATGTGCTTGCTGCTGCCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 492

AATTACAAATGGGCCTGTCACAGGAAGGGCTGGTGATGTGCTTGCTGCTGCCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

AATTACAAATGGGCCTGTCACAGGAAGGGCTGGTGATGTGCTTGCTGCTGCCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

AATTACAAATGGGCCTGTCACAGGAAGGGCTGGTGATGTGCTTGCTGCTGCCAACACAGCAGCAGAAGTCGCAATGCGGCTTGTGAGACCTGGGAAGAAAgtaagtgttt ... atatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgatttgttcatttcgttggtatttatatatatatatatatatatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG
 tactgat  putative branch site (score: 330)
              atttcgttggtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttttgcaaagcccaaagttttgtttcacaagttatattttatcaatcattgttcccttatccttaagcatatatctttgaaagatgtttcaagtggtgatctaactaagtatttcctttctcattttttacatgtactgatttgttcatttcgttggtatttatatatatatatatatatatattcagAATAAGGATGTTACTGAAGCAATTCAGAAAGTTGCTGCTGCTTATGATTGCAAAATTGTGGAAGGTGTTCTTAGCCATCAACTGAAACAATTTGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG