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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgttttttatttcttctaaactacagccttgtgctgtcagatctcattttccctgggagtccagtcgttgtcttattctttagtaattctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC

Basic information

species Zea mays
transcript GRMZM2G043198_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 9
gtaatttgtttttt--atttcttctaaactacagccttgtgctgtcagatctc-attttccctgggagtcca--gtcgttgtcttattctt---tagtaat-tctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC
||| |||  ||||   |  | | ||  ||   |    | |||    |||  || |||||       |  |||     ||| |||||||  |   ||  ||| ||| |  |||||| ||||||||||| |||||||| ||  |||||||||||||||| |||||||| || ||||||||||| |||||||||||| | |||||||| || || |
gtagtttccttttgcaaaatatactgtacagtatagatatgcaactagacatctatttttaacaacatgccatcactgttttcttattactatatatcaatatcttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC

upper sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaatttgttttttatttcttctaaactacagccttgtgctgtcagatctcattttccctggga-gtccagtcgttgtcttattctttagtaattctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC
          | | |    || || | | |   |||||      | | ||  ||    |||  | ||  | ||      || ||||||  |||     || | ||||||| |||||||| |||||  | ||||| ||  |||| || || ||||| || ||||||||||| | |||||||||||| || |||||||| ||||| |
---------gtatgaagatttttagatttctctcttgt------aaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaa---aatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC
















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|31356807|gb|CD441164.1|CD441164
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|149060160|gb|EE157128.2|EE157128
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|6056687|gb|AW091092.1|AW091092
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|32801932|gb|CD954168.1|CD954168
EST:     GCCGCAGATAAACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
EST: gi|110221099|gb|EC902997.1|EC902997
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|32829371|gb|CD969049.1|CD969049
EST:     AAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: AAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|71431245|gb|DR812295.1|DR812295
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|148928998|gb|EC874173.2|EC874173
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|32788226|gb|CD940462.1|CD940462
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGGTGGATAGAGCTACTATTA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
EST: gi|76282095|gb|DV021663.1|DV021663
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|31349832|gb|CD434189.1|CD434189
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|50330846|gb|CO525972.1|CO525972
EST:     TGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: TGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|67038743|gb|CO464998.1|CO464998
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|5761992|gb|AI967040.1|AI967040
EST:     CCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: CCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|60396979|gb|DN229798.1|DN229798
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|463331|gb|T18298.1|T18298
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|71316610|gb|DR794980.1|DR794980
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|32801690|gb|CD953926.1|CD953926
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
EST: gi|5566803|gb|AI881669.1|AI881669
EST:     ACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: ACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|31349833|gb|CD434190.1|CD434190
EST:     GCCCCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|14245208|gb|BG873790.1|BG873790
EST:     CCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: CCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|18177942|gb|BM379152.1|BM379152
EST:     CAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: CAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|6031329|gb|AW076186.1|AW076186
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|78086374|gb|DV514767.1|DV514767
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|78092118|gb|DV520492.1|DV520492
EST:     GCCGCTGATATACTGCCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|60340342|gb|DN207315.1|DN207315
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATTTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|15082843|gb|BI389527.1|BI389527
EST:     TGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: TGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|32802072|gb|CD954308.1|CD954308
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTA
EST: gi|211383123|gb|FL435718.1|FL435718
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|40336329|gb|CK370399.1|CK370399
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|71432758|gb|DR813808.1|DR813808
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|44900498|gb|CK827043.1|CK827043
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|148951825|gb|EC897588.2|EC897588
EST:     GCCGCTGATTATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATTTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGA-TATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|60340970|gb|DN207943.1|DN207943
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|6828052|gb|AW331695.1|AW331695
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|5566870|gb|AI881781.1|AI881781
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
EST: gi|37378649|gb|CF626026.1|CF626026
EST:     GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAG                         GTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA
genomic: GCCGCTGATATACTGGCCAAGGAAGGTATCAGTGCCGAGgtaatttgtt ... ctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttccctgggagtccagtcgttgtcttattctttagtaattctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC
                                           ttctctgttc  CT-rich tract
                             ttattctttagtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgttttttatttcttctaaactacagccttgtgctgtcagatctcattttccctgggagtccagtcgttgtcttattctttagtaattctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG