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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTCTGCTCATGGGACCCACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttctggttattactttccatagtacatgatgaacttatttatgagtttgcggtagttgtatatttgttattttgaaatatcataattgtttttttttacag

Basic information

species Oryza sativa
transcript LOC_Os06g02550.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02550.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G864414_T02 (Zea mays), 5'ss of exon 14
TGGCTCTGCTCATGGGACCCACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttctggttattactttccatagtacatgatgaacttatttatgagtttgcggtagttgtatatttgttattttgaaatatcataattgtttttttttacag
||||| |||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||| ||  |||||   |    ||| |||| |  || | ||||| |  |     ||   |    | |||   ||   ||  |      |   |                 
TGGCTTTGCTCATGGGACCCACGAAGAAGGCCAACAGCAGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgtcatacttctg---acagttttacatactggattaagaactaacctgc---ttcatgaccttcgtac-cttaccatcattgtgctttgcag----------------
















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|29638209|gb|CB643218.1|CB643218
EST:     GTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTTTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: GTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|58685705|gb|CK074392.1|CK074392
EST:     CACAAAGAAGGCCAACAGCGGTGGAGG-TTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|88691087|gb|CI735166.1|CI735166
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|88691956|gb|CI735531.1|CI735531
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|218500572|gb|FG950928.1|FG950928
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|58678822|gb|CK067509.1|CK067509
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCC
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCC
EST: gi|66916087|gb|CX102935.1|CX102935
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|29641486|gb|CB646493.1|CB646493
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|58687727|gb|CK076414.1|CK076414
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATCCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|58685041|gb|CK073728.1|CK073728
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAAC
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAAC
EST: gi|29685601|gb|CB681876.1|CB681876
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|88689214|gb|CI732790.1|CI732790
EST:     CACAAACAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAANAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|88691942|gb|CI735517.1|CI735517
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
EST: gi|88688550|gb|CI732126.1|CI732126
EST:     CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAG                         CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT
genomic: CACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttc ... ttttttacagCCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTCTGCTCATGGGACCCACAAAGAAGGCCAACAGCGGTGGAGGTTTTGCAGCATCCCTTCTTTCAGgttatttttctggttattactttccatagtacatgatgaacttatttatgagtttgcggtagttgtatatttgttattttgaaatatcataattgtttttttttacag

- - - - - - - - - - - AAAGAA
- - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - TGGAGG