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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttgcatcaaatatttgagttcatttattagtcttttttcagtcgatttgagtatgagcatctttattggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCTGCAGTACTTAAGGATGGATCTGTAGTTGAAGCTGATACA

Basic information

species Zea mays
transcript GRMZM5G828229_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g05570.3 (Oryza sativa), 3'ss of exon 9
gtaattgttgcatcaaatatttgagttcatttattagtcttttttcagtcgatttgagtatgagcatctttattggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCTGCAGTACTTAAGGATGGATCTGTAGTTGAAGCTGATACA
||||| | | | |||| |   |  ||| | ||     | |||| |||    |||||||     | || |||  |   ||||||||||||||||| || ||||||| ||||||||||||||| |||||||| |||||||||||| | |||||||||||||||||||||||||||
gtaatagcttcgtcaagttcatttgtttaatt-----tattttgtcaacatatttgagctcatgtatattttgttccaaccagGGAGCTCTTATTGATAAACTTGAAGCTGGCTCTGATGGTAGGGTGTCATCTGCAGTACTTGAAGATGGATCTGTAGTTGAAGCTGATACA
















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|60346312|gb|DN213285.1|DN213285
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
EST: gi|32847653|gb|CD987334.1|CD987334
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
EST: gi|18660451|gb|BM500869.1|BM500869
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGC-CTTATCGAAAA-CTTGGAGCTGGCTCTGATGGAAGGGTG-CTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
EST: gi|211294189|gb|FL028349.1|FL028349
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
EST: gi|71439564|gb|DR820614.1|DR820614
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT
EST: gi|213168062|gb|FM185604.1|FM185604
EST:     CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAG                         GGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGANNNNNGTCTTCT
genomic: CTAAGAAGTATGAGGAACTGTATCAGCAAAATGGTGTCAAATTCATAAAGgtaattgttg ... tggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattagtcttttttcagtcgatttgagtatgagcatctttattggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCTGCAGTACTTAAGGATGGATCTGTAGTTGAAGCTGATACA
                                      tctttatt  CT-rich tract
                                     atctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttgcatcaaatatttgagttcatttattagtcttttttcagtcgatttgagtatgagcatctttattggtaaccagGGAGCTCTTATCGAAAAACTTGGAGCTGGCTCTGATGGAAGGGTGTCTTCTGCAGTACTTAAGGATGGATCTGTAGTTGAAGCTGATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT