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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATCGAGCTTGTATTGAAAGAGAAATATACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactgacattgttatgaccaatgctttatcccagatattttgtattgctagttaaataaaataattactcatagtttcagttaaatatggcttctg...

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.3 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 13
GTACATCGAGCTTGTATTGAAAGAGAAATATACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactgacat----tgttatgac-caatgctttatcccagat--attttgtattgctagttaaataaaataattactcatagtttcagttaaatatggcttctg
|| |||||||||||||| ||||||||||||||| |||||||||||||||| |||||||||||||| ||||||||||| ||||| || || |  |    || | |       ||| || ||  ||||  ||||    ||||||  ||||||||     ||| ||||  ||||  |       | |||| 
GTTCATCGAGCTTGTATGGAAAGAGAAATATACTCACTATTGGATCATCCTTTTCTCCCAACATTATATACTTCATTCCAGgtcagtcttatgtgctatgctgttgtgttgtgccttgtcttagattcatttaaggttgctaaataaataaat--ggtacacataacttcatctgc-----gtttcta
















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|702138|gb|D48429.1|D48429
EST:     ACGCACTATTGGNTCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTNTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAG
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAG
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGA
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGA
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 65 (downstream exon)
Score: 40

GTACATCGAGCTTGTATTGAAAGAGAAATATACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTG




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