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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattatctttaaatctttaatttgtcatacatcatagctagtagcttgttaaattcatcattttttctattgatggtcattttctttctcgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTACTTCCCTGCCGGCACAGAACTTTATGCAA

Basic information

species Zea mays
transcript GRMZM2G704032_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G704032_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 12
ttattatctttaaatctttaatttgtcatacatcatagctagtagcttgttaaattcatcattttttctattgatggtcattttctttctcgtc--ttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTACTTCCCTGCCGGCACAGAACTTTATGCAA
 |   |  |  | |     |    |   |  || ||     || | ||||   |       ||||| || ||| ||   |  | ||| ||  ||  ||| ||||||||||||||||||||||||| || ||||||||||||||||||||  ||||||| |||||||||||||| ||||||||
ctgaaacttccagagaggcagagagcgctg-atgatgatctgttggttgtctgaccggctctttttcct-ttgttgactaagtacttccttttccatttcagGAGAAGGTTCTTTGTAGGATTTGCTACGAGGGGGAGATATGCATGGTCTTACTTCCTTGCCGGCACAGAACATTATGCAA
















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|71761132|gb|DR959069.1|DR959069
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|149000343|gb|EE037503.2|EE037503
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|149107037|gb|EE188931.2|EE188931
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|6022166|gb|AW067094.1|AW067094
EST:     AAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|110944040|gb|EE164197.1|EE164197
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|78023713|gb|DV492100.1|DV492100
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|18659625|gb|BM500436.1|BM500436
EST:     GGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: GGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|166675211|gb|EG212155.1|EG212155
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTAT
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTAT
EST: gi|149083045|gb|EE172299.2|EE172299
EST:     CAAGTGTCCCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: CAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|148975093|gb|EE025660.2|EE025660
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGTTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
EST: gi|60356237|gb|DN223210.1|DN223210
EST:     AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAAT                         GAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA
genomic: AATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccct ... cgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttaaattcatcattttttctattgatggtcattttctttctcgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTACTTCCCTGCCGGCACAGAACTTTATGCAA
                       tattgat  putative branch site (score: 3)
                                tcattttctttctcgt  putative PPT
     taaattcatcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattatctttaaatctttaatttgtcatacatcatagctagtagcttgttaaattcatcattttttctattgatggtcattttctttctcgtcttttagGAGAAGGTTCTTTGTAGGATTTGTTATGAGGGGGAGATATGCATGGTGCTACTTCCCTGCCGGCACAGAACTTTATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT