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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacctgctacgctgtcaagttgtacattctgctatgaaccctctttgtgttaattattttgttcctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 6
gtatgctacctgct-acgctgtcaagttgtacattctgctatgaaccctctttgtgttaattattttgttcctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG
||||  | |   ||  |  | ||||  |  || |||   |||||    |     | |   |  |||||||| ||| ||||||||| | ||||||||||| || |||||||| ||||| ||||||| |||||||||||| |||
gtattttgcaaacttgcaatttcaatctaaac-ttcaattatgactttttcccatatacttacttttgttcatggcacagGGAAAGCTTTTGGTGTCACAGATTTTATTAATCCAGAAGAATTGAATGAACCTGTTCAGCAG
















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|71331902|gb|DR802836.1|DR802836
EST:     GCGTCCAAGATTATAGGAGTTGATACT-ATCCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GCGTCCAAGATTATAGGAGTTGATACTAAT-CCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|211510916|gb|FL028116.1|FL028116
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGNAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|29945503|gb|CB815672.1|CB815672
EST:     GAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCCCGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|5296121|gb|AI782996.1|AI782996
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|89246725|gb|DY618512.1|DY618512
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|6194720|gb|AW146824.1|AW146824
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|5895803|gb|AW037049.1|AW037049
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|211510917|gb|FL028117.1|FL028117
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|76016067|gb|DT943237.1|DT943237
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|71325642|gb|DR799508.1|DR799508
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
EST: gi|6020665|gb|AW065698.1|AW065698
EST:     GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG                         GGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC
genomic: GGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAAC

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), 43 (downstream exon)
Score: 79

GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGGgtatgctacc ... cctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtacattctgctatgaaccctctttgtgttaattattttgttcctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG
                             tgttaat  putative branch site (score: 132)
                                      ttttgttcct  putative PPT
                         tttgtgttaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctacctgctacgctgtcaagttgtacattctgctatgaaccctctttgtgttaattattttgttcctggtacagGGAAATCATTTGGTGTCACGGACTTTATTAACCCAGATGAATTGAGTGAACCTGTTCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG