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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaggtctatattccttgttgataagttctcttctgtgaagcagactggtctatcatgcctaaccatttttgccttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 14
gcaggtctatattccttgttgata-----agttctcttctgtgaagcagactggtctatcatgcctaaccatttttgccttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA
    |||  ||||| || ||| ||     | ||     || |||     ||| ||  || |   ||||  |||||  || ||||  |||||||||||| ||||||||||||||||||||||||| || |||||| |||| ||||| ||  || | ||||||| | | ||| ||| |
----gtccgtattcgttattgttatgcagaattgcagactatgacatgaacttgtggataaatactaaa-attttctccatttcttatgcagCTTGTTTTACTTCTGCTTGCTCTGGTGTCTGTTCCCTGGATGCTGATCCCAAAGCCATTTTTCTTGAAGATGGAGCATGAGCGA
















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|94475016|gb|EB703974.1|EB703974
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|32807350|gb|CD959584.1|CD959584
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGGCAGAAGACAGT                         GCAGCTTGTTCTGCTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|78080517|gb|DV508929.1|DV508929
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|94480098|gb|EB709056.1|EB709056
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGGTTGA
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATG-TTGA
EST: gi|211366578|gb|FK956887.1|FK956887
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|76283841|gb|DV023409.1|DV023409
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|211366579|gb|FK956888.1|FK956888
EST:     CAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGA
genomic: CAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAG-AAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGA
EST: gi|91050182|gb|EB160600.1|EB160600
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|78123326|gb|DV541710.1|DV541710
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAAAAGACAGT                         GCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
EST: gi|32809734|gb|CD961968.1|CD961968
EST:     CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGGCAGAAGACAGT                         GCAGCTTGTTCTGCTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT
genomic: CCAACAGATGAGATTGGTGAAAACCAGTTGTTTAGTGGCCAGAAGACAGTgcaggtctat ... cttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttctgtgaagcagactggtctatcatgcctaaccatttttgccttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA
                             gcctaac  putative branch site (score: 2)
                                   ccatttttgccttttc  CT-rich tract
                                     attttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaggtctatattccttgttgataagttctcttctgtgaagcagactggtctatcatgcctaaccatttttgccttttccaatGCAGCTTGTTCTACTTCTGCTTGCTCTGGTGTCTGTGCCTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA