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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctcttcacttcctctctcaatcctaatgaaggcatttcggagtcatgtgatgtgcgcatgctacag

Basic information

species Zea mays
transcript GRMZM2G069676_T02
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 17
GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtag--ttctcttcacttcctct-----ctcaatcctaatga--aggcatttcggagtcatgtga-tgtgcgcatgctacag
||||| ||||||||||||||||| ||||||||  || || | || || ||||| || ||||||||||| ||||| |||||     || |||  |    |||     | ||| |||    |  |  |||||    | |||||||   || |||||| ||||
GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAGgtcagcctccctttgccctatctgaaatcccaagccttccaatcatccatttaactgacatgtgaacatgtgcatgc-acag

upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA10G35490.2 (Glycine max), 5'ss of exon 16
GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctcttcacttcctctctcaatcctaatgaaggcatt-tcggagtcatgtgat--gtgcgcatgctacag----------------
||  | ||||| || |||||||| |||||| | || ||  | || || ||||||||||| |||||||| ||||||||||||     | ||||  |   | |         |  | ||| | |   |   |||  |    | |  |  ||  |                 
GTCCGAGTTTCTGGCTATGGTGGATGGTTCCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAGgtaaaggccctcacggctagtgttggggtgtttatatgcaatattaaaacaatgcaactgattcagagactgaacatacttgttactgtag

upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA20G32030.1 (Glycine max), 5'ss of exon 16
GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctcttcacttcctctctcaatcctaatgaaggcatttcggagtcatgtgatgtgcgcatgctacag----------------
||  | ||||| || |||||||| |||||  | || ||  | || || ||||||||||| |||||||| ||||||||||||    || ||||  |   | |   |  |  | | |  || |   |   |||  |      ||  ||                    
GTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAGgtaaaggtcctcacagctagtgttggtgttt-ttatgcaatattaaaacaatgcaactgattcagactgatcatacttgttactgtag

upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 16
lower sequence: AT5G17530.1 (Arabidopsis thaliana), 5'ss of exon 18
GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctcttcactt--cctctctcaatcctaatga--aggcatt---tcggagtcatgtgatgtgcgcatgctacag
 |  | ||||| || | |||||| |||||  | || || || ||||| |||||||||||||||||||| ||||| ||||||    | |  |     | |  || | |   | |    |  | ||   ||| | |  |    ||  ||||        
ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatatgtataaagcttaacttagtttcagtatctaaactttcactcgaatttttcaattggacgcag-------

upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 5'ss of exon 17
GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgta--gttctcttc--acttcctctctcaatcctaatga--aggcatttcggagtcatgtgatgtgcgcatgctacag
||  | | ||| || | ||| || |||||| | || || ||||| || ||||| |||||||||||||| ||||||||||||   | | |||   | |  | |  | | |  |||| |  ||  |||| | | | |    || || | |  | | ||
GTTCGAGCTTCTGGCTTTGGGGGATGGTTCCTTCTAAGACTCTCCCTTCATGACCCTGTTCTTCCCCTTAACATTGAGgtataatcccctttcaagtgtcacgttaagttataattaccagatattttgcactgaca--atatgagaactccatag

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|211441849|gb|FL182586.1|FL182586
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACARAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|76289293|gb|DV028861.1|DV028861
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|78112841|gb|DV531235.1|DV531235
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|86465999|gb|DY232372.1|DY232372
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|101389186|gb|EB816548.1|EB816548
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGACGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|67018791|gb|CO447540.1|CO447540
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|20512826|gb|BQ280024.1|BQ280024
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|32928442|gb|CF033254.1|CF033254
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCCTTGCGGTTCCTGCTGC
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGC-TTGCGGTTCTTGCTGC
EST: gi|32928208|gb|CF033020.1|CF033020
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
EST: gi|32929540|gb|CF034352.1|CF034352
EST:     TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG                         GCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT
genomic: TCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCT

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: 45 (upstream exon), 42 (downstream exon)
Score: 17

GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCTGTGAATGAATTTCCAGCACTGGATGTGACGGCACTGAACAAATTCGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCTGTGAATGAATTTCCAGCACTGGATGTGACGGCACTGAACAAATTCGTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 23

GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCTGTGAATGAATTTCCAGCACTGGATGTGACGGCACTGAACAAATTCGTGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 34

GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAGgtagttctct ... catgctacagGCACAGAGTAACGATGATGCGATTAAGCTGGGGCTTGCGGTTCTTGCTGCTGTGAATGAATTTCCAGCACTGGATGTGACGGCACTGAACAAATTCGTGC