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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgtattaattttggtgttgtgtaatggtaatatatgattatatgtttatgtactggtgaattttgtgcggattagttttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g59600.2 (Oryza sativa), 3'ss of exon 1
ttttttgtattaattttggtgttgtgtaatggtaatatatgattatatgtttatgtactggtgaattttgtgcggattagtt-ttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGA-AGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG----------------------------
                          | |  | | |||  | | ||    || |||  || |  ||| ||||    |   || | || |  |  |  | |||  |  |        |   |  |   || | | | ||||||  ||||  |||||||||||||||||||| ||||||||||| || ||||||||||| || |                            
--------------------------tgagcgcagtatggggtgat---cttctgttttgattgattgtgtggatgtggattatagacagctaatccttagggttttttcgtgttttcttcaggagtagATAACACAGAATAG-TTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC

upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 1
ttttttgtattaattttggtgttgtgtaatggtaatatatgattatatgtttatgtactggtgaattttgtgcggattagtt-ttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGA-AGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG----------------------
                     |||  | |  | | |||  | | ||    || |||  || |  ||| ||||    |   || | || |  |  |  | |||  |  |        |   |  |   || | | | ||||||  ||||  |||||||||||||||||||| ||||||||||| || ||||||||||| || |                      
-------------------cattgc-tgagcgcagtatggggtgat---cttctgttttgattgattgtgtggatgtggattatagacagctaatccttagggttttttcgtgttttcttcagGAGTAGATAACACAGAATAG-TTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGA
















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|22819364|gb|BU499454.1|BU499454
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|91049728|gb|EB160146.1|EB160146
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211461819|gb|FL074147.1|FL074147
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211461826|gb|FL074154.1|FL074154
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|22819427|gb|BU499517.1|BU499517
EST:     AGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGACCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: AGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|93284362|gb|EB676626.1|EB676626
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|22819362|gb|BU499452.1|BU499452
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211064278|gb|FK983495.1|FK983495
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCGCTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211461823|gb|FL074151.1|FL074151
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211064280|gb|FK983497.1|FK983497
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|22819430|gb|BU499520.1|BU499520
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|21843523|gb|BQ704104.1|BQ704104
EST:     CGCGAGGCCATAGTTGCATCATTCCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: CGCGAGGCCATAGTTGCATCATT-CGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211064283|gb|FK983500.1|FK983500
EST:     ATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: ATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|50333782|gb|CO528908.1|CO528908
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211064277|gb|FK983494.1|FK983494
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|26456267|gb|CA827850.1|CA827850
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|211464348|gb|FL074165.1|FL074165
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCAGCACCAG                         GACTGATCTCCTCACTAGGGGCGTAGAGGTGAAGAGAAGAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|5566922|gb|AI881833.1|AI881833
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|19770380|gb|BQ035101.1|BQ035101
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCACCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|149084419|gb|EE173874.2|EE173874
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAG                         GACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG
genomic: TCGCGAGGCCATAGTTGCATCATTCGCCTGAGACGACTGCCCACCGCCAGgtatgcggca ... ttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttatgtactggtgaattttgtgcggattagttttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG
                                           ttttgttttc  CT-rich tract
                              attagttttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgtattaattttggtgttgtgtaatggtaatatatgattatatgtttatgtactggtgaattttgtgcggattagttttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGAAGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG