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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcactttaacagtgaatatatcagtgatgttggaaacttgttcttatgcagcacttttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTTGGATTATCAGGTCTAGGTTTTGGTGGTGGATTTGAAAGGCTGCATTATC

Basic information

species Zea mays
transcript GRMZM2G075488_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075488_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06820.1 (Oryza sativa), 3'ss of exon 3
---------------gtaagtcactttaacagtgaatatatcagtgatgttggaaacttgt-tcttatgcagcacttttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTTGGATTATCAGGTCTAGGTTTTGGTGGTGGATTTGAAAGGCTGCATTATC
               |||| |   |||     |   | | |  ||||  |||||||||||| ||||  ||| || || | ||| ||||||  ||||||||| |||||| ||||||| ||||||||| ||||||| ||||||||||| ||| | || |  ||||| ||||||||||||||||||||||
gtaagtcattcttaagtaaatactttttgtgttttttttctatgtgaatttggaaacttgtatcttgagcatcatttgtgttttcagGTTTCTCTTCCATCAGGTGGCAGGTTAACTCCTAAGATGTTGCAGTGCCTTGGATTATCTGGTTTGGGCTCCGGTGGAGGATTTGAAAGGCTGCATTATC
















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|71430371|gb|DR811421.1|DR811421
EST:     AGGTCGTTCATGAGGTTATAAGACACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|60358578|gb|DN225551.1|DN225551
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|211492404|gb|FL232704.1|FL232704
EST:     TCATGAGGTTATAAGACACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: TCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|67011936|gb|CO440685.1|CO440685
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|78090093|gb|DV518467.1|DV518467
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|149107818|gb|EE292179.2|EE292179
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|149075976|gb|EE164545.2|EE164545
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCCTCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT
EST: gi|148995979|gb|EE035228.2|EE035228
EST:     AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGG                         GTTCTTCTTCCATCTGGTGGCCGGGTAACCCCTAAGATGCTGCAGTGTCTT
genomic: AGGTCGTTCATGAGGTTATAAGATACTTAAGTGAATCTGAAGGGGGAGGGgtaagtcact ... ttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatatatcagtgatgttggaaacttgttcttatgcagcacttttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTTGGATTATCAGGTCTAGGTTTTGGTGGTGGATTTGAAAGGCTGCATTATC
                                        cactttttttt  CT-rich tract
                                         actttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcactttaacagtgaatatatcagtgatgttggaaacttgttcttatgcagcacttttttttgcagGTTCTTCTTCCATCTGGTGGCCGGTTAACCCCTAAGATGCTGCAGTGTCTTGGATTATCAGGTCTAGGTTTTGGTGGTGGATTTGAAAGGCTGCATTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA