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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcattttcatttgttctgttcccatctgactttgagtgataggtacctatcctaacacttctttctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG

Basic information

species Zea mays
transcript GRMZM2G099255_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 4
gttaatcattttcatttgttctgttcccatctgactttgagtgataggtacctatcctaacacttctttctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG
||||||||||||| ||||||||  |||    | |   |   |  ||| | | || ||||| ||||  |||| ||| ||| ||||| |||||||||||||| |||||| ||||||| ||||| ||||| |||||  |||| |||||||||||
gttaatcattttcttttgttcttatcct---taatcatatct--tagatccataccctaatactttgttctcattacagCTGTGTACCACTTCATAACTTTGATTATGTATATAGCTATCTTATGGAAACAAATATCAGCTTTGTTGACTG
















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|78105512|gb|DV523930.1|DV523930
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|78090001|gb|DV518375.1|DV518375
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|76018436|gb|DT945606.1|DT945606
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|101398462|gb|EB821104.1|EB821104
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|86474172|gb|DY240542.1|DY240542
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|78093093|gb|DV521467.1|DV521467
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|14997232|gb|BI319245.1|BI319245
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATA
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATA
EST: gi|86471048|gb|DY237418.1|DY237418
EST:     GCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: GCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|71774867|gb|DR972745.1|DR972745
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTCTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|78077573|gb|DV506007.1|DV506007
EST:     ATGCCCTACAAGATCTTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: ATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|101388829|gb|EB816396.1|EB816396
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|148961000|gb|EE011700.2|EE011700
EST:     CAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|71767366|gb|DR965303.1|DR965303
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|211278467|gb|FL480336.1|FL480336
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGAKBATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|149106921|gb|EE188822.2|EE188822
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|71442672|gb|DR823722.1|DR823722
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTCTGTCTTGCTCTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|76912823|gb|DV164898.1|DV164898
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|86469460|gb|DY235830.1|DY235830
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|149082889|gb|EE172120.2|EE172120
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|50337694|gb|CO532820.1|CO532820
EST:     GAAAACCAGCAATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: GAAAACCAGC-ATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|76912822|gb|DV164897.1|DV164897
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
EST: gi|148963210|gb|EE014187.2|EE014187
EST:     CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAG                         TTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC
genomic: CATGCCCTACAAGATCCTGAAAACCAGCATTTTGTCTTGCTTTCTGAGAGgttaatcatt ... ctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccatctgactttgagtgataggtacctatcctaacacttctttctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG
                                    cacttctttct  CT-rich tract
                                          tttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcattttcatttgttctgttcccatctgactttgagtgataggtacctatcctaacacttctttctaattgcagTTGTGTGCCACTTCATAACTTCGATTATATATATAGTTATCTCATGGAGACAAACGTCAGTTTTGTTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA