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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAATTACTAGTGCAGCTGCTTTGTTAAAACAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagttggtttattgtaacatccatgatccatgtaatagtattgattcattggcttgttgcgaaggaaccatgttatggcatgattaggcagatt...

Basic information

species Oryza sativa
transcript LOC_Os06g41360.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 7
GAACAATTACTAGTGCAGCTGCTTTGTTAAAACAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagttgg-tttattgta-acatccatgatccatgtaatagtattgattcattggcttgttgcgaaggaaccatgttatggcatgattaggcagatt
| ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||| ||||||||| | ||||||||||| |||||||||   |||||| ||||| | |   |    || |    ||| |  |  || | ||    ||   ||    ||   ||| |    |||   |     |  | 
GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagttggctttatcgaatgtacttctggttttggtattttttatggt-cacatcctatatgatgtggcttcatctctgagcactttctaatattt-
















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|16579174|gb|BI813269.1|BI813269
EST:     TGCTTGTAGCACACATGCCTGGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTG
genomic: TGCTTGTAGCACACATG-CT-GTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTG
EST: gi|86494938|gb|CI137571.1|CI137571
EST:     CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|88955926|gb|CI092214.1|CI092214
EST:     AGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: AGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|29646780|gb|CB651787.1|CB651787
EST:     CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|86865656|gb|CI335399.1|CI335399
EST:     GCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: GCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|86494957|gb|CI137590.1|CI137590
EST:     CTATGCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: CTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|29681206|gb|CB677481.1|CB677481
EST:     CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
EST: gi|88248553|gb|CI248402.1|CI248402
EST:     CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAG                         CCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagt ... gtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAATTACTAGTGCAGCTGCTTTGTTAAAACAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGgtttggcagttggtttattgtaacatccatgatccatgtaatagtattgattcattggcttgttgcgaaggaaccatgttatggcatgattaggcagatt

- - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG