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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgatatgttgtcatgtataattatgctgaatatctggcactaagaatctttgtgtataacccactcacagttcttttttttccttccccaataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG

Basic information

species Zea mays
transcript GRMZM2G037342_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 2
ctgatatgttgtcatgtataattatgctgaat-atctggcactaagaatctttgtgtataaccca-ctcacagttcttttttttc-cttccccaataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG
     || ||    |    |||| || |  || || |     | |  ||   |  | |      | || || |||| |||||||| ||| |         |||||||||||| ||||||||||| || || || |||||||| ||||||||  ||||||||||  |||| ||| | |||||||| | |||||| ||||| |
---taatcttccagtaggaaattctgttacatcatttaaagtttaacattagtcagcaaggtgaagcttactgttcctttttttctctttctttcctgagcagGTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCG

upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 2
---------------ctgatatgttgtc--atgtataattatgctgaatatctggcac-----taagaatc--tttgtgtataacccactcacagttcttttttttccttccccaa------------taagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG
               |  |   | ||||  ||| || ||| | || | ||  ||||||     | | |||   ||||||| |  |  |     |||| || || | | |    |||            ||  ||||||| || ||||| ||||||||||| |||   ||||||||||| ||||| |||||||| |  ||||| || || ||   || ||   | ||| |  | |
gtaaagttttcagcaccaactagctgtctaatgaatcattgt-ctaattaattggcaccccaatgaaaattattttgtgttttcctgatctctagttgttcttgtacttagagcaaggtatacatgattattccagGTTTCAGGTGAAAAAGAAACAGTTTTTTGTTAACTTCATTACCATTACCCTGTTTGGAGTTGTTGGTACATTAATAAGTTGTAGCATCATAACTTTCG
















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|211187214|gb|FL054036.1|FL054036
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|148996402|gb|EE035697.2|EE035697
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|78119306|gb|DV537690.1|DV537690
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGNNNNNNNNNCAGTTCTTTCAAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|71315380|gb|DR794294.1|DR794294
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|76921052|gb|DV168433.1|DV168433
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|50328971|gb|CO524097.1|CO524097
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
EST: gi|148931601|gb|EC874712.2|EC874712
EST:     GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGG                         GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT
genomic: GAGGACCTCTTCTTTATTTACCTGCTGCCGCCGATCATATTCAATGCAGGgtacggaatt ... aataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctttgtgtataacccactcacagttcttttttttccttccccaataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG
                 cactcac  putative branch site (score: 2)
                   ctcacagttctttttt  CT-rich tract
                          ttctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgatatgttgtcatgtataattatgctgaatatctggcactaagaatctttgtgtataacccactcacagttcttttttttccttccccaataagccagGTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTG

- - -atgttgt
- - - - - - catgtat
- - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - ctggcac