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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccttgattcctgttaccttgatgctccaaaaattcctatatgttgcaagagttttaatatttcatttcctgcttgcaaagtgtatttatgtaaagtcaaaaacatttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACAGCCTTATTGGAAGCTTTTC

Basic information

species Oryza sativa
transcript LOC_Os07g46450.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G340359_T01 (Zea mays), 3'ss of exon 9
gtgccttgattcctgttaccttgat--gctccaaaaattcctatatgttgcaagagttttaata---tttcatttcctgcttgcaaagtgtatttatgtaaagtca---aaaacatttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACAGCCTTATTGGAAGCTTTTC
|| ||||   |    ||| | ||||  | |   | || |  || |||||  |||||||| ||||   ||||  |||||||||||  | ||| |  ||||| |  ||   |  |  | ||||||||||||||| || || || ||||||||||| || || ||||||||||| ||||| |||||||||||||| |
gtaccttt-ctgtaattatcatgatatgttgttataactatta-atgtta-aagagtttcaatagtttttcccttcctgcttgcccactgtctgaatgtatacacatgtatgatgtatctgcagCATGTTCTCCGGGAGCTTCCATCTTCTCCTGTTCCAGCTTCCTGCTGTACAGCATTATTGGAAGCTTTCC

upper sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 9
-----gtgccttgattcctgttaccttgatgctccaaaaattcctatatgttgcaagagttttaatatttcatttcctgcttgcaaagtgtatttatgtaaa-gtcaaaaacatttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACAGCCTTATTGGAAGCTTTTC
      | |  | |||    | || | | || |  |||  ||     |||||  || |  || || ||      | |||||| |  | |||||  | ||| |  || |  | || ||||||||||||||| ||||| || ||||||||||| || || ||||| ||||| ||||| |||||||||||||| |
gtacctttctgtaattatcatcacgt-gttgttataaaggtta----atgtt--aaaaagttcaaaatcg----ttctgcttacccactgtatgaacgtatacatctatgatatatctgcagCATGTTCTCCGTGAGCTTCCATCTTCTCCTGTTCCAGCTTCGTGCTGTACAGCATTATTGGAAGCTTTCC
















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|44679468|gb|CR292902.1|CR292902
EST:     GACTGTGTAAAG                         CATGTTCTACGTGAACTACCTTCTTCTCCAGTACCTGCTTCCTGCTGCACA
genomic: GACTGTGTAAAGgtgccttgat ... atttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACA
EST: gi|58671855|gb|CK060541.1|CK060541
EST:     CGGAGTTTGCACAGGATGAGGATGCTCATGTTATTGGTGACTGTGTAAAG                         CATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACA
genomic: CGGAGTTTGCACAGGATGAGGATGCTCATGTTATTGGTGACTGTGTAAAGgtgccttgat ... atttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACA
EST: gi|88422394|gb|CI689211.1|CI689211
EST:     CGGAGTTTGCACAGGATGAGGATGCTCATGTTATTGGTGACTGTGTAAAG                         CATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACA
genomic: CGGAGTTTGCACAGGATGAGGATGCTCATGTTATTGGTGACTGTGTAAAGgtgccttgat ... atttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcatttcctgcttgcaaagtgtatttatgtaaagtcaaaaacatttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACAGCCTTATTGGAAGCTTTTC
                                            catttct  CT-rich tract
                      tgtatttatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccttgattcctgttaccttgatgctccaaaaattcctatatgttgcaagagttttaatatttcatttcctgcttgcaaagtgtatttatgtaaagtcaaaaacatttctgcagCATGTTCTACGTGAACTACCATCTTCTCCAGTACCTGCTTCCTGCTGCACAGCCTTATTGGAAGCTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG