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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagtatgtctcggttatgaaagttgggtacgactcctcagttttttccacatcggtaaaaccgaatttctttaccatgtaacgaaattacaaggt...

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 5'ss of exon 2
ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagtatgtctcggttatgaaagttgggtacgactcctcagttttttcca--catcggtaaaaccgaatttctttaccatgtaacgaaattacaaggt
||||||| ||||| ||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||    ||   ||   | || ||     |     | |  || | || |  |  ||   ||      | ||   |  ||   | || |      ||    
ATTTGTACGAGAAGGGGGAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCGCTGCACCTCGGCCATCTCATCCCCTTCATGTTCACCAAgtaagcgcgattgttccaatctgcaatactcgctgtcccctgcaatgttcttgattcactcgtgttgttgtataaata-actgggcaatgccgcggcagta-
















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|67015552|gb|CO444301.1|CO444301
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|148959767|gb|EC905658.2|EC905658
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|67037924|gb|CO464466.1|CO464466
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|149010069|gb|EE041876.2|EE041876
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|71305908|gb|DR789081.1|DR789081
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|148935574|gb|EC879617.2|EC879617
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|211230962|gb|FL341122.1|FL341122
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTKACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|149105517|gb|EE291042.2|EE291042
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|9953035|gb|BE639618.1|BE639618
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|149073834|gb|EE162156.2|EE162156
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|67014073|gb|CO442822.1|CO442822
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
EST: gi|148973279|gb|EE024361.2|EE024361
EST:     TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAA                         ATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA
genomic: TCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

ATTTGTATGAGAACGGGCAGAAGTTCTACCTCTACACGGGGAGGGGGCCCTCGTCGGAGGCCCTGCACCTCGGCCACCTCATCCCCTTCATGTTCACAAAgtaagtagta ... ctttcttcagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT