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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcggtcccaaatttcacttttaacatgattatatgcttctgggtttcttcctgcctaactcacatttgatctcaatag

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcggtcccaaatttcacttttaacatgattatatgcttctgggtttcttcctgcctaactcacatttgatctcaatag
||||||||| ||||||||||| || || || |||||||| ||||||||  ||||||||||  |||| ||| | |||||||| | |||||| ||||| |||| |||   | ||    || |  ||| || ||   || | ||| || | |  |  ||  |   |  |||||  ||| ||    
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcct--ctttaaattttacctggc-atgttcttttgtgctcatctctctcactcgtacattccatcacag---
















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|93016611|gb|EB642131.1|EB642131
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATAT
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATAT
EST: gi|148996402|gb|EE035697.2|EE035697
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|78119306|gb|DV537690.1|DV537690
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|71315380|gb|DR794294.1|DR794294
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|76921052|gb|DV168433.1|DV168433
EST:     CTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: CTGTTTGGTGCAGTTGGCACCTTGATCTCTTTT-ACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|32866161|gb|CF005843.1|CF005843
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCTTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|50328971|gb|CO524097.1|CO524097
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
EST: gi|148931601|gb|EC874712.2|EC874712
EST:     ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG                         GCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG
genomic: ACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAG

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: 407

GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcgg ... atctcaatagGCGCTCTAGGACTAATATCAAGGCTTAATATCGGCGCACTTGAACTGGGAGACTATCTTG