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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaggatcataggactaaacctatttatcgtgctgtttatgctgtgctatatgttataagtcagtgtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G015344_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 4
gtatgttcaggatcataggactaaacctatttatcgtgctg-tttatgctgtgctatatgttataagtcagtgtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
||||| |     | | |||| ||||||| |||| | || || |||||     |  | |    |||||||  ||||| |||||||| |||||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||||| ||| ||||||||||
gtatgcttccatttacagga-taaacctgtttagcatgttgctttatatgccgtgacagaggataagtc--tgtctgtgttcttt-cttagGCCATCAAAAGGGACCCTTCCTTTGCAAGTAAGGTGAAGAAAATAGTTGTACTGGGTGGTGCTTTCTTTGCGGCTGGAAATGTCAGCCCAGCTGCTGAAG

upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 4
-------gtatgttcaggatc-ataggactaaa----cctatttatcgtgctgt----ttatgctgtgctatatgttataagtcagt-gtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
       |||  ||   |||   ||| |||  |    ||  |   || |    |    || |  |   |||  | |  | | |   | || ||  |||  |  |||||| |||||||| ||  |||||||||||||||| || |||| ||||||| |||| ||||| || ||||||||    || ||||| || |||||||| ||||
gtaagctgtacattgttgatttgtagtactctatggtcccgtccttcataacttcaaattgtagttgcctacgtttgttgatttgatagtgtcacttccattattagGCAATCAAAAGGGATTCTTCCTTTGCAAGCAAAGTGAAGAGAATAGTTATACTTGGTGGTGCATTCTTTGCCTTGGGGAATGTGAATCCTGCTGCAGAAG

upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttcaggatcataggactaaacctatttatcgtgctgtttatgctgtgctatatgttataagtcagtgtctctgttctttgctta--gGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
      | || |||||      || ||  |   |    ||  |||   |  | | | |||  | |  |  || |   ||| |||  |||  |||||||||| | ||   ||| ||||| |||||||| |||||||| ||| | || ||||||||||||||| |    ||||||||||| ||||| ||||| |
-----gtaagaatcatg-----aatcccctcctttaatcttcttaaaatccgatttgtgtactga--cgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG

upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g03690.t01 (Vitis vinifera), 3'ss of exon 4
--------gtatgttcaggatcataggactaaacctat--ttatcgtgctgtttatgctgtgctatatgttata--agtca---gtgtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
           | | | |     |  |   ||  || |  || || || | |   | |||   |  ||   ||    ||||      | | | ||  ||| |||||| || ||||| ||| | |||||||| |||||||| |||||  | || ||||| ||||| |||||||||||    ||||||||||| |||||||| ||||
gtaagttgcggtatcctgtcctttcagttcaattctgtgattttcatggtctgagttctgcaatgcataccattctggtcacacaaatgtatttttattgattagGCTATTAAAAGGGACTCGTCCTTTGCGAGCAAGGTGAAGAAGGTGGTCGTACTTGGTGGTGCTTTCTTTGCACTGGGAAATGTCAATCCTGCTGCCGAAG

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|89759746|gb|DY688465.1|DY688465
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|71318567|gb|DR796043.1|DR796043
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|71449461|gb|DR830511.1|DR830511
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|76935894|gb|DV174515.1|DV174515
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|71438819|gb|DR819869.1|DR819869
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|78105410|gb|DV523828.1|DV523828
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|94473161|gb|EB702119.1|EB702119
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|149077634|gb|EE166336.2|EE166336
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTT
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTT
EST: gi|76290576|gb|DV030144.1|DV030144
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|71439185|gb|DR820235.1|DR820235
EST:     CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTA
EST: gi|211057431|gb|FL062179.1|FL062179
EST:     CAGGAGAAGTCTCTGTGCTTGCGTTGGGACCC-TGACAA-TGTAGCATTG                         GC-ATCAAAAGAGCCCCT
genomic: CAGGAGAGGTCTCTGTGCTTGCGTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... ctttgcttagGCCATCAAAAGAGACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgtttatgctgtgctatatgttataagtcagtgtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG
                                     tctctgttctttgctt  CT-rich tract
                  tatatgttataagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcaggatcataggactaaacctatttatcgtgctgtttatgctgtgctatatgttataagtcagtgtctctgttctttgcttagGCCATCAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG