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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGATAAGCTTGTTTCTGAAGGTACCTTGCACCATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattggtggttgtccttgtcactctgatctgcatacagagtttttcttgcatatgtactcactgacatttattatctccttcatgttag

Basic information

species Oryza sativa
transcript LOC_Os07g46790.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044480_T01 (Zea mays), 5'ss of exon 6
CTAGATAAGCTTGTTTCTGAAGGTACCTTGCACCATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattggtggttgtcct--tgtcactctgatctgcatacagagtttttcttgcatatgtactcactgacatttattatctccttcatgttag
|| || || ||| ||||||||||||| || |||||||| |||||| |||| ||||||||  | ||||||||||||||||| ||||||||||||    |||||  |  ||||  ||||| ||||  | ||   |  |||    ||| || |   |||||||  || | |            
CTTGACAAACTTATTTCTGAAGGTACTTTACACCATGATGTTATACGTTTTCATTACTATGTTCAGTACCATCTATATATACAAgtaagtatttcctgttgttgtattgtcgttctgaactgctcatagtactactctcatgtatttattt-ttgacattatttttttag----------

upper sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G136803_T02 (Zea mays), 5'ss of exon 2
CTAGATAAGCTTGTTTCTGAAGGTACCTTGCACCATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattggtggttgtcct--tgtcactctgatctgcatacagagtttttcttgcatatgtactcactgacatttattatctccttcatgttag
|| || || ||| ||| ||||||||| || ||||||||| ||||| |||| ||||||||  | ||||||||||||||||| |||||||||||||   |||||  |  ||||| ||||  ||||  | ||   |  |||    ||| || |   ||||||| ||| |    |   | ||||
CTTGACAAACTTATTTGTGAAGGTACTTTACACCATGACATTATACGTTTTCATTACTATGTTCAGTACCATCTATATATACAAgtaagtattgcctgttgttgtattgtcattctgcactgctcatagtactactctcatgtatttattt-ttgacatt-atttttatttgttttttag
















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|58667917|gb|CK056603.1|CK056603
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
EST: gi|7134681|gb|AU082619.1|AU082619
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
EST: gi|58665534|gb|CK054220.1|CK054220
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGCAA
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAA
EST: gi|66915772|gb|CX102620.1|CX102620
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
EST: gi|58659146|gb|CK047826.1|CK047826
EST:     TGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATAGTGTGCAA                         TTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGG
genomic: TGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATA-TATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGG
EST: gi|58690658|gb|CK079345.1|CK079345
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAGTTA                      
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGC-A---Agtaagtattg ... ttcatgt
EST: gi|58690658|gb|CK079345.1|CK079345
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAGTTA                      
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGC-A---Agtaagtattg ... ttcatgt
EST: gi|58674228|gb|CK062914.1|CK062914
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGA
EST: gi|58671568|gb|CK060254.1|CK060254
EST:     ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAA                         TTATCAGAGGCAGCTGCCTATGC
genomic: ATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGC

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: 70 (upstream exon), 61 (downstream exon)
Score: 15

CTAGATAAGCTTGTTTCTGAAGGTACCTTGCACCATGACGTTATATGTTTCCATTACTACATCCAGTACCATCTATATATGCAAgtaagtattg ... ttcatgttagTTATCAGAGGCAGCTGCCTATGCAAGGAAGAAAAAGGTTATTCTGAAAGGAGATTTACCTATTGGTGTTGATAGGAATAGTGTGGATACTTGGGTATACC




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