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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcatatagttgtcattatttattagtaaaccgagttttctttttaggaggctgtccatggtatgtgttttaacttctattctcttgtttcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG

Basic information

species Zea mays
transcript GRMZM5G877316_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877316_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 1
tagcatatagttgtcattatttattagtaaaccgagttttctt----tttaggaggctg--tccatggtatgtgttttaacttctattct-cttgtttcctgt--gcagCTCGAAGGAGAAGCCCACTCTTGG
          |   | ||||    |  | |   || |||  |     ||   || | ||  | | || | | || |  || |||| || | | | |||  |||  ||||||||||||||||||||||||||||
---------atacgccttatgccatgatcacttgaatttcatccaaattggagatgatgctttcttgttgtctgatccaatttctcttttacctattttttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
















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|18662176|gb|BM501785.1|BM501785
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|50331541|gb|CO526667.1|CO526667
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|78108789|gb|DV527206.1|DV527206
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|76912266|gb|DV164646.1|DV164646
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|61117466|gb|DN558427.1|DN558427
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGGTCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|71428140|gb|DR809190.1|DR809190
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|19436862|gb|BM953272.1|BM953272
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|211134644|gb|FL028665.1|FL028665
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|76287488|gb|DV027056.1|DV027056
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|19057519|gb|BM736186.1|BM736186
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|19057686|gb|BM736353.1|BM736353
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|19436861|gb|BM953271.1|BM953271
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|78084791|gb|DV513184.1|DV513184
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|78084825|gb|DV513218.1|DV513218
EST:     CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: CCAAGCAAGCGACACTCTTGTCCTCTCCGCGCCAGATCGTTGTTTATGAGgtacggatca ... tcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggaggctgtccatggtatgtgttttaacttctattctcttgtttcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG
                       ttttaac  putative branch site (score: 2)
                             cttctattctcttgtt  CT-rich tract
                       ttttaacttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcatatagttgtcattatttattagtaaaccgagttttctttttaggaggctgtccatggtatgtgttttaacttctattctcttgtttcctgtgcagCTCGAAGGAGAAGCCCACTCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC