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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaag

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 11
GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaag
||| ||||||||||| |||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||  ||||  ||     |  |    || | ||   |    | | |    |   | |   | ||    | |     || ||   ||||                                                          
GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAGgtagctttt-tttaccaatgcatccaacatctttactttccaggcaatcctgtaaattttgtaactgcaatagtaaccctattttc-tggttcactgaag---------------------------------------------------------

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 11
GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaag
||| ||||||||||| |||||||| |||||||||||||| ||||| |||||| |||||||||| |||||||||||||||||||||||  | |  | |  ||||   |   |  ||||||  |  |  |  |     ||||||   ||| | |||   |      |||   ||||    | | | |  | ||                                            
GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagctttttatca--attcattcaccatc--tttacttaccag--gcaatctgtaaaaattttcaactgcaatagcaata-----atgccgtttt----ctggttctctgaag-------------------------------------------
















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|211131287|gb|FL186946.1|FL186946
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAAGTTCTTTGGACTATG
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAA-TTCTTTGGACTATG
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|78179069|gb|DV549442.1|DV549442
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|211131286|gb|FL186945.1|FL186945
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|149014218|gb|EE043773.2|EE043773
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|149105261|gb|EE290752.2|EE290752
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTTCA-GAGTGGGAAATCAAT
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTT-CAAGAGTGGGAAATCAAT
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGAC-ATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|78087725|gb|DV516118.1|DV516118
EST:     TTAAATTTGATTGCTCGGCTTC-ACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTTCA-GAGTGGGAAATCAATAGAAGCCGATTATTCTTTGGACTATG
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTT-CAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATG
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     GTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: GTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|7238183|gb|AW573405.1|AW573405
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGC

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: 125

GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 496

GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 204

GTTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG