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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctgtacagacggatgattcagcatgtcgtggtgttctatttatgttgctcggcaacgtctctagtcgtgcagcctactcactgcttgtaattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG

Basic information

species Zea mays
transcript GRMZM2G035417_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035417_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g15360.1 (Oryza sativa), 3'ss of exon 1
---ttgctgtacagacggatgattcagcatgtcgtggtgttctatttatgt-tgctcggcaacgtctctagtcgtgcagcctactcactgcttg---taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG
    || |||  |   || |||| | |||        ||||  || | ||| |||| ||  | |   ||| | ||||    |||| || ||| |   |  ||| ||||| ||||| |||||||| ||||||||||  ||||| || |||| |   |||| |||||| ||||| ||||||||| ||||||||||||||||||||||||
tggctgttgtcaatgtggttgatgctgca-------atgtttaatgtgtgtatgcttggatatgggactatttgtgccttatacttacagctagctctgttttgcagGTGGCTGAGGTGAAGAGAATCATTGAGAGTACTCAGGGGCAGAATGTGTACCCGGCGGATCAGCAGATGCTCATACACCAAGGGAAAATTCTCAAGGATG
















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|29130299|gb|CB381003.1|CB381003
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|71448259|gb|DR829309.1|DR829309
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|78121958|gb|DV540342.1|DV540342
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|211524988|gb|FL195256.1|FL195256
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCGTCG                         GTTGCTGACGTGAAGAGGATCATTGAGACCACTCAGGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|211524987|gb|FL195255.1|FL195255
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCGTCG                         GTTGCTGACGTGAAGAGGATCATTGAGACCACTCAGGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|78107573|gb|DV525991.1|DV525991
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|9825075|gb|BE575292.1|BE575292
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|5566780|gb|AI881646.1|AI881646
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|94472331|gb|EB701289.1|EB701289
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|20803264|gb|BQ294314.1|BQ294314
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|91876714|gb|EB406671.1|EB406671
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|211524983|gb|FL195251.1|FL195251
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|74244160|gb|DT652074.1|DT652074
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|76908411|gb|DV162927.1|DV162927
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
EST: gi|89763929|gb|DY690917.1|DY690917
EST:     AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCG                         GTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC
genomic: AGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTAC

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: 45 (upstream exon), 49 (downstream exon)
Score: 176

GGAGAGTTCAAGGACCGAGGCGGCGTCGGGCGAGATGAAGCTTAACGTCAAGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 201

GGAGAGTTCAAGGACCGAGGCGGCGTCGGGCGAGATGAAGCTTAACGTCAAGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 91

GGAGAGTTCAAGGACCGAGGCGGCGTCGGGCGAGATGAAGCTTAACGTCAAGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 229

GGAGAGTTCAAGGACCGAGGCGGCGTCGGGCGAGATGAAGCTTAACGTCAAGACCCTCAAGGGCACCAACTTCGAGATCGAGGCGAGCCCCGATGCATCGgtacggcccc ... taattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgctcggcaacgtctctagtcgtgcagcctactcactgcttgtaattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG
                                tactcac  putative branch site (score: 229)
                                                ttttc  putative PPT
                                          ttgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctgtacagacggatgattcagcatgtcgtggtgttctatttatgttgctcggcaacgtctctagtcgtgcagcctactcactgcttgtaattttcagGTTGCTGATGTGAAGAGGATCATTGAGACCACTCAAGGTCAGAGTACCTACCGGGCGGACCAGCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- gctgtac
- - - - - - - - - - -cagcatg
- - - - - - - - - - - - - - - -tggtgtt
- - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttg