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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCAATCGACCTTAACCAGCAGGGGGTCTACACCATTGTGATTGGGAGTCACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagttcattgactgccttggaatcaatggatacttcaatctacagtgccatgttagacgcagagttttttgctcttctatgttcaaattgtact...

Basic information

species Oryza sativa
transcript LOC_Os01g12870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G062826_T01 (Zea mays), 5'ss of exon 2
CACCAATCGACCTTAACCAGCAGGGGGTCTACACCATTGTGATTGGGAGTCACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtac--taaagttcattgactg--ccttggaatcaatggatacttc-aatctacagtgccatgttagacgcagagttttttgctcttctatgttcaaattgtact
  || |||||||| |||||||| |||||||||| |||||| || ||||| ||||| ||  | ||||| ||||||||||| ||||| ||||||||||||||||     |||  |  ||  |||  |  |     | | |  |  ||  || |||  |      | | | | || |   ||||| |    |  || |||        
GTCCCATCGACCTCAACCAGCAAGGGGTCTACAGCATTGTCATCGGGAGCCACATTTCCACCATCTATCACTATGGCTTCGCAAACCTTATGATGCGCAGgtgtggcaaacctacttttctgatcactatggcctacgattgtttagaacctagtgcattgaggttggcacacatagttttgatacctttagtacaagaa-----

upper sequence: LOC_Os01g12870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G153181_T01 (Zea mays), 5'ss of exon 2
CACCAATCGACCTTAACCAGCAGGGGGTCTACACCATTGTGATTGGGAGTCACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtac--taaagttcattgactgccttggaatcaatggatacttcaatctacagtgccatgttagacgcagagttttttgctcttctatgttcaaattgtact
| || |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| || ||||||||||| ||||| ||||| ||||||||||||||||     ||   |  ||  |||         || ||  |  |   |  |||||     | |   |  | |||    ||  | || ||  |   ||   | | 
CGCCCATCGACCTCAACCAGCAAGGGGTCTACACCATTGTCATTGGGAGCCACATCTCAGCCATCTACCACTACGGCTTCGCAAACCTTATGATGCGCAGgtgtggcaagcctacttttctgaacctagtgcattgagttttggcacatacagcttagtttctaattc-gaggggattagtattgtacatcataaggttgc-
















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|58683238|gb|CK071925.1|CK071925
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTG
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTG
EST: gi|87015516|gb|CI303122.1|CI303122
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAAT
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAAT
EST: gi|163926065|gb|EG715021.1|EG715021
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
EST: gi|38568572|gb|CD670787.1|CD670787
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
EST: gi|58679806|gb|CK068493.1|CK068493
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
EST: gi|58677292|gb|CK065979.1|CK065979
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
EST: gi|33678949|gb|CF307188.1|CF307188
EST:     CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAG                         ATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA
genomic: CACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAA

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: 53 (upstream exon), 71 (downstream exon)
Score: 35

CACCAATCGACCTTAACCAGCAGGGGGTCTACACCATTGTGATTGGGAGTCACATCTCTGCTATCTACCACTATGGCTTTGCAAATCTTATGATGCGCAGgtactaaagt ... cttctggtagATATGCTGAAGCCATACGTGAATTCAACAAAATCTTGCTGTACATTCTGAAATATAAGCAGTACCATCAGAAGTCCCCGCAGTATGACCAGATCTTGAAG




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