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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcagctctcagtttacaactgtttgtggctgctatcccaagaaacaactgtgaccctggttctgaactaactgttcgatatttgcatatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC

Basic information

species Zea mays
transcript GRMZM2G134389_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134389_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g10650.1 (Oryza sativa), 3'ss of exon 4
gtaag----atcagctctcagtttacaactgtttgtggctgctatcccaagaaacaactgtgaccctgg--ttctgaactaactgttc-gatatttgcatatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC
|||||    ||||| || ||   || |        | ||||| ||        | | |    || |||   | || |||| |||| ||  || ||| | ||||| |||||||| || || ||  | || ||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| ||| 
gtaagcttaatcagttcccacactaaactctgcaattgctgccattatcttccaaagcaagaactctgagatcctaaactgactgctccaatgtttccctatcttcagCACCGCACCGGCTGCGTCGTGGGGTGCTTGAGGAAGCTTCAGAAATGGTGCTTGTCTTCAGTGTTCGACGAGTACCAGCGCTTCGCCGCTGCGAAGGCGA

upper sequence: GRMZM2G134389_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtaagatcagctct--cagtttacaac-tgtttgtggctgctatcccaagaaacaactgtgaccctggttctgaactaactgttcgatatttgcatatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC
                                            |||| |    | ||  || | || ||| | |||||     ||| ||     |     | |   |     | || | |  || | |  ||||| | |   ||||||||||||| ||||| ||||| || ||||  || ||  |||| |||||||||||||| || ||||| || || ||||| |||||||| || || |||||  
gtgagatttttgctgaattttcttttaaaatatttttgtaataagtaatagtgtcactaacaatataaaacgtttttgtaatatctaaccatgtgaggttttcttgtcaaaagtatgtaatttct-tcctttattttc-tgcatgcagCACCGAACAGGTTGCTTGGTAGGATGCTATAGAAAATTGCAAAAATGGTGCTTGTCATCCGTCTTTGATGAATACCAACGCTTTGCAGCCGCCAAAGCAA

upper sequence: GRMZM2G134389_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G43550.2 (Glycine max), 3'ss of exon 4
gtaagatcagctctcagttt-----acaactgtttgtggc-----tgctatcccaagaaacaactgtgaccctggttctgaactaactgttcgatatttgcat--atctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC
|| ||||     ||   |||     | ||   ||| || |     |  ||    | | |  |||| | |  ||  ||   |     |  ||   |  ||   |   | ||||||||||||| ||||| || || || ||||  || ||  |||| |||||||||||||| || ||||| || || ||||| |||||||| ||||| |||||  
gtgagatttttgctggattttttttaaaaacatttttgtcataagtattagtatatgcactaactat-attcttattaaaagtatgcaatttcttccttctttctgtgtgcagCACCGAACGGGTTGCTTAGTAGGATGCTATAGAAAATTGCAAAAATGGTGCTTGTCATCTGTCTTTGATGAATACCAACGCTTTGCAGCTGCCAAAGCAA

upper sequence: GRMZM2G134389_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G05000.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagatcagctctcagtttacaactgtttgtggctgctatcccaagaaacaactgtgaccctggttctgaactaactgttcgatatttgcatatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC
||||      | |||   |   ||   |||    ||  | || | |  |   |    ||   ||  | |   |||| | |     || || | || ||||||| || || |||||| | || || |||||||||||||| ||||||||||| ||| | ||  | |||||||||||||| || ||||| || ||||||||  
gtaaatcattcactccaatcctaaacattt-catcttttgtctccaccactgaagaagaaaatgagttt---ctaagtat---gaatctgga-atttgcagCATCGGACCGGTTGTCTTGTTGGTTGCTTGAGGAAGCTCCAGAAATGGTGTTTGACATCGATATTCGACGAGTACCAACGATTTGCAGCAGCGAAAGCTA

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|211509867|gb|FL433772.1|FL433772
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
EST: gi|5555286|gb|AI881237.1|AI881237
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGTTGTT-GGTCGGGTGCTTGAGGAAGCT
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCT
EST: gi|5555280|gb|AI881231.1|AI881231
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGNTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
EST: gi|5555378|gb|AI881329.1|AI881329
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
EST: gi|93281321|gb|EB673585.1|EB673585
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
EST: gi|50339825|gb|CO534951.1|CO534951
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
EST: gi|32845463|gb|CD985144.1|CD985144
EST:     ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAG                         CACCGAACTGGCTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC
genomic: ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGC

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: 44 (upstream exon), 46 (downstream exon)
Score: 80

ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 182

ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 222

ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 83

ACCCAAGAAACCAACCTCTGCTTATTCATTGTAAGAGAGGCAAGgtaagatcag ... atatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacaactgtgaccctggttctgaactaactgttcgatatttgcatatctgcagCACCGAACTGGTTGTTTGGTCGGGTGCTTGAGGAAGCTGCAGAAATGGTGCTTGTCTTCAGTCTTCGACGAGTACCATCGCTTTGCCGCTGCGAAAGCGC
                        aactaac  putative branch site (score: 83)
                                     atattt  TA-rich tract