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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC

Basic information

species Zea mays
transcript GRMZM2G158479_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 8
gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC
||||  | |||   ||||   | |  ||  ||  | |||| || ||||||| || |    || |||| ||  ||| | |||| ||  |    ||||||||||||||||||||||||| ||||| ||||| || ||||||||||| || |||||||| |||||||||||||| ||| ||||||| || ||||||||||
gtaatcagctc--aactt---ttgtcca--tttatatattact-ttcaattcgcaat---atttcctaataccaacctactctaa--tttgatgtagATGGGAGTGAAATGGATCTTCCTACTGTCACTTGCACTTCTCCAAGCCGCATACTACCGTCGCATGAGGTGGTCCGTCCTGAAGTCACGCAAGCTGGTCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 7
gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgc-tactccatatcctgatcacaatccactcaaaaatccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC
           |    ||   | |||   ||   || |   ||| |||||     || ||  | | || |  ||| |        | ||     | |||||||| | |||||||| ||| |||| ||||| || || || || |||||||| ||||||||| |||||||||||||  | ||||| || |||||||| |
----------gtccgtttcctttgctatcatgtttccac--ctaatcaataaaaatattctgttttctaactacactttttatgcatat-----gcagATGGGATTTAAATGGATATTTGTACTGTCACTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaa-atccat-tgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC
        || ||  |||     |||   ||   || | |     || ||         ||||||||| |  | | | || |     || ||| || |||||||| | |||||||| ||| |||| ||| | || || || || |||||||| ||||||||| |||||||||||||  | ||||| || |||||||| |
------gtctgttt-cttttgctgctatcatgtttccaata--gatcgataaagacacgcatatcctgttttctaactacacttgttatgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC

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|31356708|gb|CD441065.1|CD441065
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|14244836|gb|BG842774.2|BG842774
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|166544398|gb|EG296822.1|EG296822
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCG
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCG
EST: gi|67028963|gb|CO457712.1|CO457712
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGA-AAAGCTG                         ATGGGAGTGAA-TGGATCTT-CTACT
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACT
EST: gi|16379087|gb|BI992745.1|BI992745
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|15323508|gb|BI478611.1|BI478611
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|60338899|gb|DN205872.1|DN205872
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|211036752|gb|FL261404.1|FL261404
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|74245922|gb|DT653836.1|DT653836
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|91054777|gb|EB165195.1|EB165195
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTTTACTATCACTAGCGCTTCTCCAAGCTGTC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|76283401|gb|DV022969.1|DV022969
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|16919521|gb|BM074230.1|BM074230
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|15590213|gb|BI674829.1|BI674829
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|31356905|gb|CD441262.1|CD441262
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|60396397|gb|DN229266.1|DN229266
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTTTACTATCACTAGCGTTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|14243082|gb|BG840790.2|BG840790
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|149097934|gb|EE183875.2|EE183875
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|6012601|gb|AW062038.1|AW062038
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|31354314|gb|CD438671.1|CD438671
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|18163834|gb|BM333673.1|BM333673
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|78075104|gb|DV503538.1|DV503538
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
EST: gi|40303643|gb|CK348030.1|CK348030
EST:     TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC
genomic: TATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... tccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC
                     tcctgat  putative branch site (score: 3)
                                      tcaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTCCAAGCTGCCTACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGAAAGCTGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG