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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctttgacacctgcttctgtggaactcttatatcagttttcattttttgttttcatcaagagagcacttattagtagtttatttaatttaaatatatcattaaaatgctagaagggcggatcagtgatggatagctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGTAAAAGCTGCTATAGTTACCTGTGGAGGTCTATGTCCTGGTTTGAATGAT

Basic information

species Zea mays
transcript GRMZM2G139360_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139360_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g34050.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------gtat-gttttctttgacacctgcttctgtggaactcttatatcagttttcattttttgttttcatcaagagagcacttattagtagtttatttaatttaaatatatcattaaaatgctagaagggcggatcagtgatggatagctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGTAAAAGCTGCTATAGTTACCTGTGGAGGTCTATGTCCTGGTTTGAATGAT
                                                     || ||||  |   | |  || ||  ||   ||  | |||||||||| ||  ||  |  || |        ||| || ||| | |||||||  | |||| |   | ||    || ||  || ||     |  ||||  |||| ||| |||||||| ||||| ||||| || || ||||||||||||||||| |||||||||||||||||||| |||||||| |||||||| || || ||||||||||| |||
gtatatttctcatcacttatgagttagtagctctttcgattctgctaatatacattgtttcttcaaatatttgattacgtattaca-tcatatcagtttccaccttcagcgttta--------gcagttgttaattgtttattagacttaatt-cgttat----attcttaaatggtaaggcgttgataaatagttttatgtagGGTACATCGTGCAGGCCCTCGTAAGGAGATATACTATGAACCAGAGGAAGTAAAAGCTGCCATAGTTACTTGTGGAGGGCTCTGCCCTGGTTTGAACGAT

upper sequence: GRMZM2G139360_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttttctttgacacctgcttctgtggaactcttatatcagttttcattttttgttttcatcaagagagcacttattagtagtttatttaatttaaatatatcattaaaatgctagaagggcggatcagtgatggatagctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGTAAAAGCTGCTATAGTTACCTGTGGAGGTCTATGTCCTGGTTTGAATGAT
                                     ||     |||    |||||| | |  | |         | ||| |     ||||   ||||  |   |  ||  | ||||        || ||    ||     |||| |  |||||| ||||| || || |||||  ||||||||| || |||||| | |||||| |||||||  || |||||||||||||| || ||||||||| | ||||||
-----------------------------------caatggggctttctcatttttggtgttgtaagtgagctggtgattggggtagtattgtgtttatcttcttgttttgattgct--------ggttc--ccat-----gcttcc--tagGGTACATCGTGCTGGGCCACGTGAGGAGATATTCTTTGAGCCTGGGGAAGTGAAAGCTGGAATTGTTACCTGTGGAGGGCTCTGTCCTGGTCTCAATGAT
















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|76021503|gb|DT948673.1|DT948673
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
EST: gi|93280916|gb|EB673180.1|EB673180
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
EST: gi|71757783|gb|DR955720.1|DR955720
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
EST: gi|71435418|gb|DR816468.1|DR816468
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
EST: gi|101399831|gb|EB821762.1|EB821762
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGT
EST: gi|211381885|gb|FL378668.1|FL378668
EST:     TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATG                         GGTGCATCGAGCA
genomic: TCTGCTGGAGCAGAGTGTGTTGATCTTGACTGTAGCTGGGTGGAGCAATGgtatgttttc ... ctttctgtagGGTGCATCGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatatcattaaaatgctagaagggcggatcagtgatggatagctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGTAAAAGCTGCTATAGTTACCTGTGGAGGTCTATGTCCTGGTTTGAATGAT
                                             ctttctgt  CT-rich tract
     tatcattaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttctttgacacctgcttctgtggaactcttatatcagttttcattttttgttttcatcaagagagcacttattagtagtttatttaatttaaatatatcattaaaatgctagaagggcggatcagtgatggatagctttctgtagGGTGCATCGAGCAGGACCACGCAAGGAGATATACTATGAGCCAGAGGAAGTAAAAGCTGCTATAGTTACCTGTGGAGGTCTATGTCCTGGTTTGAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG