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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtagccgccccccaccctcaaccgaacctctgccgggtcctgatctggtcgttgcccgcgggggagctcgtcttgtgtaccgtcctgacggttttctcttctcgatgtggttgcagACTGCTGCCTCGCGCTGTGGTG

Basic information

species Zea mays
transcript GRMZM2G060564_T02
intron # 1
splice site 3'
intron type U2

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|211520836|gb|FL034043.1|FL034043
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|37416319|gb|CF645810.1|CF645810
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520841|gb|FL034048.1|FL034048
EST:     CAACGTCTGGCACACCGACHTGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520834|gb|FL034041.1|FL034041
EST:     CAACGTCTGGCACACCGACATGACTAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520840|gb|FL034047.1|FL034047
EST:     CAACGTCTGGMACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397639|gb|FL034039.1|FL034039
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397637|gb|FL034037.1|FL034037
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|148930645|gb|EC872835.2|EC872835
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520833|gb|FL034040.1|FL034040
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211397638|gb|FL034038.1|FL034038
EST:     AACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCAMCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: AACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCC-CCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520838|gb|FL034045.1|FL034045
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520842|gb|FL034049.1|FL034049
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|101396680|gb|EB820265.1|EB820265
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520837|gb|FL034044.1|FL034044
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|76011810|gb|DT938980.1|DT938980
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCT                         ACTGCTGCCTCGCGCTGTGGTG
genomic: CAACGTCTGGCACACCGACATGACGAACGCCATCCAGGCCGACTTCCCCTgtacgtagcc ... gtggttgcagACTGCTGCCTCGCGCTGTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggagctcgtcttgtgtaccgtcctgacggttttctcttctcgatgtggttgcagACTGCTGCCTCGCGCTGTGGTG
                     tcctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtagccgccccccaccctcaaccgaacctctgccgggtcctgatctggtcgttgcccgcgggggagctcgtcttgtgtaccgtcctgacggttttctcttctcgatgtggttgcagACTGCTGCCTCGCGCTGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC