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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctttctcaaactgcagcacctaaagattacacaatataataagtcatattgattttcaagcctatattgcagacaagtaccaaacataaaaacattcctttccctgctacaacatgggtctgactgagaacaattattctctgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 12
TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctttctcaaactgcagcacctaaagattacacaatataataagtcatattgattttcaagcctatattgcagacaagtaccaaacataaaaacattcctttccctgctacaacatgggtctgactgagaacaattattctctgtttatgcag
|||||||| |||||||| |||||||  ||||| ||||||||||||||||| || |||||||  ||||||||||||||||| || ||||||||| ||||||||          ||| |  || |  |  ||||  || | | | ||   | |   | | |    |  |   |  | |    ||  |||||          ||||  ||| ||||| | | | ||  | |  | ||||    |||
TTCACAAGGTCAGGCCACACTCAACTCCCTAGTAATGCTATCATGATCACTAGTACAATCACTGTTGTTCTTTTCAGCACGATGgtaagttctctctcaaac----------aaacacaaccctgtgcaatacatcct-tcggttcaaagggagacagt----atgaaagctgatccctgaacaattcc----------acaagttggttctga-taaaatcatctctcttatgttccctcag

upper sequence: GRMZM2G037342_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 14
TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctttctcaaactgcagcacctaaaga--ttacacaatata-ataagtcatattgattttcaagcctatattgcagacaa-gtaccaaacataaaaacattcctttccctgctacaacatgggtctgactgagaacaattattctctgtttatgcag
||||| |  || || || |||  ||  |  |||||||| ||||||||||||||||| ||||  ||||| |||||||||||| | ||||| | ||| |     || ||   || |     |||  || | |  ||  ||    ||| | ||  ||  ||| |||        | | ||   |||   |                                                            
TTCACCATGTCGGGGCACACTTCACTGCGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTGgtaagatatttgtt---ttgtagtttctgacatccttagccagtgtccattggtttctttgttattagaggttattttgtctttgttgcatcactgatattca------------------------------------------------------------

upper sequence: GRMZM2G037342_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 14
TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctttctcaaactgcagcacctaaaga--ttacacaatata-ataagtcatattgattttca-agcctatattgcagacaa-gtaccaaacataaaaacattcctttccctgctacaacatgggtctgactgagaacaattattctctgtttatgcag
||||| |  || || || |||  || |   |||||||| ||||||||||||||||| ||||  ||||| |||||||||||| | ||||| | ||| |     || ||   || |     |||  || | |  ||  ||  | || ||      ||  ||| |||        | | ||   ||||                                                               
TTCACCATGTCGGGGCACACTTCACTAAGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTGgtaagatatttgtt---ttgtagtttctgacatccttagccagtgtccattggttttttttatcagaggaggttattttgtctttgttgcatcactgataatc-------------------------------------------------------------

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|71426857|gb|DR807907.1|DR807907
EST:     TCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: TCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|50328970|gb|CO524096.1|CO524096
EST:     TCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: TCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|19058280|gb|BM736947.1|BM736947
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|110481107|gb|EE010953.1|EE010953
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|71759365|gb|DR957302.1|DR957302
EST:     TTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: TTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|76931825|gb|DV172864.1|DV172864
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|76921050|gb|DV168432.1|DV168432
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|38568958|gb|CF974843.1|CF974843
EST:     ATGCTATCATGATCACAAGCACAATCAGTGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|87152007|gb|DY396796.1|DY396796
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|211218746|gb|FL457360.1|FL457360
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|20300776|gb|BQ163719.1|BQ163719
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|76912609|gb|DV164817.1|DV164817
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|18964390|gb|BM660978.1|BM660978
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|7216796|gb|AW562918.1|AW562918
EST:     ATGCTATCATGATCACAAGCACAATCAGTGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCCCTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|149058821|gb|EE156842.2|EE156842
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
EST: gi|78119305|gb|DV537689.1|DV537689
EST:     ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT                         GTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG
genomic: ATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGG

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), 48 (downstream exon)
Score: 87

TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGGCACCTATCCAGGGAACCAAGCGCCCTTTCTGAACCTTCCAGCCCGAAGT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 13

TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGGCACCTATCCAGGGAACCAAGCGCCCTTTCTGAACCTTCCAGCCCGAAGT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 30

TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGGCACCTATCCAGGGAACCAAGCGCCCTTTCTGAACCTTCCAGCCCGAAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 91

TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATTgtaagttctt ... gtttatgcagGTCTTTGGGCTGCTGACGAAGCCACTGATCAGGCTCTTGATCCCGTCAAGGCACCTATCCAGGGAACCAAGCGCCCTTTCTGAACCTTCCAGCCCGAAGT