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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAATGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctctttgccttgtagcatcacttttcaccaccaccaccaccatcatcatcaattgcttcgttttacag

Basic information

species Oryza sativa
transcript LOC_Os01g49770.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G122223_T01 (Zea mays), 5'ss of exon 2
ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAATGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgt--ctctttgccttgta----gcatcacttttca-ccaccaccaccaccatcatcatcaattgcttcgttttacag
|| | ||||||||||||||||||  |  |||||||||||| ||||||||| || |||||||||||||||||||| ||||||||||||||||||||||| |||  | | ||| ||  ||    | |||  | ||   || |  ||| ||     || ||||    ||| | ||  |||
ATAAGGATGTTTCAGACAAGAGTGTTACTGGGAGGAATGAACATGTATGACCGCTACCAGGATTGGCGCCTTGACGTTGATAACATGACATACGAGgtatgtacccccttggctcttaatttgtatctgtgtttgtccgctgccatcagt-caatgatcagacactttgcttcgcag

upper sequence: LOC_Os01g49770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G843389_T01 (Zea mays), 5'ss of exon 2
ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAATGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgt--ctctttgccttgtagcatcacttttcaccaccaccaccaccatcatcatcaattgcttcgttttacag
|| ||||||||||||||||||||| |  |||||||||||| |||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||  |     | || | |||||   |    |  |||| |  ||| ||   | || | ||    ||||  ||   ||
ATAATGATGTTTCAGACAAGAGTTTTACTGGGAGGAATGAACATGTACGATCGCTACCAGGATTGGCGCCTTGATGTAGATAACATGACATACGAGgtacgcagtcccttacgttgta--tttgtgtagcaccgctgccatcagt-tgatgaccagacacttcccttcttag

upper sequence: LOC_Os01g49770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G31170.1 (Glycine max), 5'ss of exon 3
ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAA---TGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgt-ctctttgccttgtag-------catcacttttcaccaccaccac-caccat-catcatcaattgcttcgttttacag-------------------------------
|| |||||  |||    |||| |  || |||| |||    | |      | || |  |     || ||| | |||||||||||||||||| ||||||||||  |   |||||  | |||         ||| | ||||       |   |     ||   |  | |||| | |  || | ||                                
ATAATGATAATTCGAGGAAGAATAATGATGGGGGGACGATTTAATTCACACGACCAATTTAGAGACTGGAGACTTGATGTTGATAACATGTCATACGAGgtgagggttctttctcctgttaaattttccattatttttagtttgtaatgcattttatgtgtgtttaattacatttttctccattgttcatcaaaatttctggtttgtctaacag

upper sequence: LOC_Os01g49770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G10930.1 (Glycine max), 5'ss of exon 3
ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAA---TGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttg---tctctttgcctt-----gtagcatcacttttcaccaccaccaccaccatcatcatcaattgcttc---gttttacag------------------------
|| |||||  ||||   |||| |  || |||| |||    |        | || |  |     || ||| | |||||||||||||||||| ||||||||||  |   ||| | | || |     ||  |||   ||||       |            ||  ||  ||||||    || | ||                         
ATAATGATACTTCAAGGAAGAATAATGATGGGGGGACGATTTGATTCACACGACCAATTTAGAGACTGGAGACTTGATGTTGATAACATGTCATACGAGgtgagagatctttctcccgttaaatgttccattgtttttattttgtaatggattttgtgtctgcacatgcttctgcattgttcatcaaaatttctggtttctgtaacag

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|300215681|gb|HO088307.1|HO088307
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|86885857|gb|CI295880.1|CI295880
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|88983372|gb|CI028608.1|CI028608
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|163920093|gb|EG709863.1|EG709863
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|702896|gb|D49187.1|D49187
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|9865627|gb|AU101377.1|AU101377
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
EST: gi|33801112|gb|CF326429.1|CF326429
EST:     ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAG                         GAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT
genomic: ATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGT

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: 69 (upstream exon), 30 (downstream exon)
Score: 7

ATCATGATGTTTCAGACAAGAGTTCTGTTGGGAGGAATGAGCATGTATGATCGGTACCAGGATTGGCGCCTTGATGTTGATAACATGACATACGAGgtttgtctct ... cgttttacagGAGTTGCTTGAGCTTGGAGATAAAATAGGTTATGTCAACACTGGATTGCGTGAGGATGAGATAGTTCGCAACCTTAGGAAGGTCAAACACCCAGCCTTTG




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