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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCCGCCTTGCTCGTGACATCGAGAAGACGTCGGACGAGGCTGCTGCCCAGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgtcgacacagtacctagagctacgagtagtaaaagaatccttgatgtagagcatttctcctcttacagcctgtgctggccaaaactttgttactgcag

Basic information

species Zea mays
transcript GRMZM2G000052_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000052_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g53190.1 (Oryza sativa), 5'ss of exon 10
CGGCCGCCTTGCTCGTGACATCGAGAAGACGTCGGACGAGGCTGCTGCCCAGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgtcgacacagtacctagagctacgagtagtaaaagaatccttgatgtagagcatttctcctcttacagcctgtgctggccaaaactttgttactgcag
 || || |||||  ||||||| || |||  ||| || |||||||||||||| || ||||| |||||||||||||||||||| ||||| || || |||||||||||| | | |||| |      | |  |    | | | ||  |   ||| |||              ||||||| ||  ||||| ||||| |||    | |||||
GGGTCGGCTTGCATGTGACATTGAAAAGCTGTCAGATGAGGCTGCTGCCCAATTTGCCTTCTCTCAGCTGAAGAAGATCCTGCCCAACGCTGCCGAGCCGgttagtatcttgacaaaaatatcaaatttg---gcaatcaagaatctctttatgctag---------ttcttacaacc-atgctgcccaaatctt----attgcag
















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|32838445|gb|CD978123.1|CD978123
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGG
EST: gi|6195066|gb|AW147170.1|AW147170
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|44900407|gb|CK826952.1|CK826952
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|86466375|gb|DY232746.1|DY232746
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCTCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|113701254|gb|EE678758.1|EE678758
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCGCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|71445884|gb|DR826934.1|DR826934
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|26557517|gb|CA829752.1|CA829752
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGG-GTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|6827827|gb|AW331470.1|AW331470
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|37377428|gb|CF625316.1|CF625316
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|6166688|gb|AW144952.1|AW144952
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|71764899|gb|DR962836.1|DR962836
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
EST: gi|154130374|gb|EC872162.2|EC872162
EST:     AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCG                         ATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG
genomic: AGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgt ... gttactgcagATAAACTACCTGGTGTCGCGCTGGGGCTCGGACGAGAACACGCTTGGTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCCGCCTTGCTCGTGACATCGAGAAGACGTCGGACGAGGCTGCTGCCCAGTTCGCCTTTTCTCAGCTGAAGAAGATCCTTCCCAATGCAGCTGAGCCGgttagtttgtcgacacagtacctagagctacgagtagtaaaagaatccttgatgtagagcatttctcctcttacagcctgtgctggccaaaactttgttactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA