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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccctaccctgctagctcgtctctttactgtaagatctaggttctatgcttttttcccctttcgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT

Basic information

species Zea mays
transcript GRMZM2G113873_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 3'ss of exon 2
gtaccctaccctgctagctcgtctctttactgtaagatctaggttctatgcttttttcccctttcgatgattc-ctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT
       | |  | |   ||  ||||    | ||    ||     |   |||  ||     |||   |||| |  || |||  |||| |       || ||     ||| ||||||||||| |||||||||||||| || ||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||| || |||||
----gtaatcacgatcaatcccctctcagatctatcgcctt--ccccccgctgcttcggtttttttctgatccatttcgtgcttttgata------tacctatcgaagGCGAGAGGCTGGGCAGAAGGATCGCCACAGACGCGATCACCACGCCAGTAGTGAACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTT
















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|149076129|gb|EE164714.2|EE164714
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|148936104|gb|EC880167.2|EC880167
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|149102766|gb|EE288113.2|EE288113
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|78110794|gb|DV529192.1|DV529192
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|76010979|gb|DT938149.1|DT938149
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|9794536|gb|BE552844.1|BE552844
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|149030074|gb|EE286293.2|EE286293
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|29130696|gb|CB381400.1|CB381400
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|93013670|gb|EB639190.1|EB639190
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|33467626|gb|CF244675.1|CF244675
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
EST: gi|101401317|gb|EB822336.1|EB822336
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccctacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcccctttcgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT
                                  ctgcctttttatct  CT-rich tract
                                       tttttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccctaccctgctagctcgtctctttactgtaagatctaggttctatgcttttttcccctttcgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATCGCCACGGATGCGATCACCACACCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT