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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttggaaacccttatgtaatactaatttgatataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC

Basic information

species Glycine max
transcript GLYMA04G37810.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
-------------------------------gttatttggaaacccttatgtaatactaa--tttgatataattatctgtgatttgaattctgagttcatctgattctttttgttt---ctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC
                                 |   | ||        ||||| ||||   |||| |  | |||| ||   |   || | ||   |    | |    |   | ||   |   ||  || |||    |     |  |  || || | ||| ||||| |||| ||||| ||||||||||| |||||||| ||||| |||  ||| || |||||  |||| ||||| ||| | ||||| |||||||||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaa-actagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-----------------------gttatttggaaacccttatgtaatactaatttga--tataattatct---gtgatttg---aattctgagttcatctga---ttctttttgtttctaagagt-tgatatatctaa-tagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC
                       ||  |   | | |    |  ||   ||| |||||  | | || | ||    ||  |||   ||||   | |||     |   | | | | |    |    || || |||    |  ||  |    |   || | |||  |||| |||| ||||| ||||||||||| |||||||| ||||| |||  ||| || |||||| |||| ||||| ||| | || || |||||||||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
gttatttggaaacccttatgtaatactaatttgatataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC
          ||   ||||| ||  |||| |      |   ||    | ||   |    ||  |     || | |          || | |  | |  | ||| | ||  |   | |  | ||| | |||||||||||||  |||||||| ||||||||||| || || ||   ||| || |||||  |||| ||||||||||| |||||  ||||||||||||
----------aaagattatg-aaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtat----------aaaaatgaagaactttaacacatctg---tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

upper sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
-----------gttatttggaaacccttatg--taatactaatttga---tataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgata-----tatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC
              |||   | |   ||||   |||||||  |||     |  ||      |    |||  | | || ||    | |    |     |  || |   ||| |     ||   |  |  ||    |||||  |||||| ||  |||| ||||| |||||||||||||||||||| ||||| |||   || || ||||| ||||||||||||||| |||||||||||||||||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaattt-cataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

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|298176430|gb|HO026665.1|HO026665
EST:     ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG                         GCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
genomic: ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAGgttatttgga ... tattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
EST: gi|9563828|gb|BE473337.1|BE473337
EST:     ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG                         GCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
genomic: ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAGgttatttgga ... tattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
EST: gi|7796615|gb|AW782012.1|AW782012
EST:     ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG                         GCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
genomic: ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAGgttatttgga ... tattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
EST: gi|151407718|gb|EV277533.1|EV277533
EST:     ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG                         GCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
genomic: ATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAGgttatttgga ... tattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTA
EST: gi|11273713|gb|BF324089.1|BF324089
EST:     TGCATTCATCAATATGATCGATCCTGGACAAATTATTCCCTTCCCACAAG                         -CTTNTCATGGG
genomic: TGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCC-ACAAGgttatttgga ... tattgtacagGCTTTTCATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctttttgtttctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC
                            atctaat  putative branch site (score: 3)
                        atatatctaatagata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttggaaacccttatgtaatactaatttgatataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA