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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCAAGGTTACCCAACGTGACAATATTATTACCCACAGAAAAGAAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaacacagattgctaatctcagtgcttgttgtttgtgttcattactagtgctgaaatcttggttttcgtccatcatctgcatttccgtttccat...

Basic information

species Oryza sativa
transcript LOC_Os10g10170.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g10170.4 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G018929_T02 (Zea mays), 5'ss of exon 11
GCGCAAGGTTACCCAACGTGACAATATTATTACCCACAGAAAAGAAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaacacagattgcta-atctcagtgcttgttgtttgtgttcattactagtg-ctgaaatcttggttttcgtccatcatctgcatttccgtttccat
|  |||||||||| ||||||||||| || ||||| ||||||||||||||||| | | ||||||||| |||||| ||||||||||||||||||||||||||  | |   |||  || ||    ||   || |     | || ||   |  || || || | ||||   |    | |    |  ||||   |||  | 
GTTCAAGGTTACCAAACGTGACAATCTTGTTACCTACAGAAAAGAAACAAGTTGACATTGATGAAAAGGAGAAAACACTTAAACTTGCTGGAAGgtgaaatcatatctattattatatggatgtttctgctagacatatttatatttgatggctaaacttttggaaattaatc-ttgctttaatttttttttaaa-
















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|25803304|gb|CA759265.1|CA759265
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58693842|gb|CK082529.1|CK082529
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|29671045|gb|CB667320.1|CB667320
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58696063|gb|CK084750.1|CK084750
EST:     TCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: TCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58691432|gb|CK080119.1|CK080119
EST:     ATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: ATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|29678934|gb|CB675209.1|CB675209
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|29614516|gb|CB619529.1|CB619529
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58689053|gb|CK077740.1|CK077740
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58692483|gb|CK081170.1|CK081170
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58694099|gb|CK082786.1|CK082786
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
EST: gi|58692218|gb|CK080905.1|CK080905
EST:     AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAG                         AGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA
genomic: AAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaac ... tgaaatgcagAGTCGGTCAAGCAGTTGGTTCCCTGCTGAGGAGATTAGGAATCAAATATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCAAGGTTACCCAACGTGACAATATTATTACCCACAGAAAAGAAACAAGTCGGCCTTGATGAAAGGGAGAAGACACTTAAACTTGCTGGAAGgtgaaacaacacagattgctaatctcagtgcttgttgtttgtgttcattactagtgctgaaatcttggttttcgtccatcatctgcatttccgtttccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG