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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatccaactccttttcatcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaaatatatatgtttctctctataatgc...

Basic information

species Oryza sativa
transcript LOC_Os11g02830.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G007283_T02 (Zea mays), 5'ss of exon 3
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatccaactccttttcatcacttcatgaatgatatcatggctgaat----agtttctgtgatcacactttttaaatatatatgtttctctctataatgc
|| || || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||||||||||||||| |||||||||||| ||||||||||||| | | | |||||| ||  || ||  |||| || |  | |||   | |    | |||   |||| |||  |  ||  || |   | || ||| |    |  
AACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttctactcctgtttgtc-ctggatgattgcttgcttggtgaactgttgattttgcttgattacaggtggtaccta-actggcttttctgttctct--

upper sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G099754_T01 (Zea mays), 5'ss of exon 3
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatccaactcctttt--------catcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaaatatatatgtttctctctataatgc
||||| || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||   | |  ||||| ||          |||     ||||||| |||||  | || |    || ||| |  |||||||| | |  || | ||    | |       
AATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaaaccttctgctcctgttatgctgtttgtcagagtgtgaatgacatcatcaccgagt----tcagtgctgccacttttttacttaatgtcttctgttttccc----

upper sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G45200.1 (Glycine max), 5'ss of exon 3
-AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatccaactccttttcatcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaaatat---atatgtttctctcta--taatgc-
 ||| | || |||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||| ||| | ||||| ||||| |||||||||| |   | |  |        ||    ||  |||   ||   || ||      || |||  |  |  | ||||   ||   ||   |||   ||||  | |||  
TAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTTCGAGGGAGTTTGGAAAATCACTTGTTCCGAagtacgg--cgagttttgccctttctaaacaaaaattcaatttcggttgg-----ttttgttcttgctttgtttaggaatggaatggatttggatctaagtgatgag

upper sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaag---aatccaactccttttcatcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaaat--atatatgtttctctctataatgc
||| | || |||||||||||||| || || |||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||||||||||||| |   | |    ||| |||  | ||  |  |   || |    ||  ||  |  |||  |     |    |||  |    |   | |      |||  ||   
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttt--tgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa---

upper sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 5'ss of exon 3
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatccaactccttttcatcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaa-atatatatgtttctctctataatgc-----
||| | || |||||||| |||||||| ||||| || || ||| || |||||||||||||||| ||||| |||||||| || ||||| ||||| || ||||||| |  |||      ||| | |  |   |||| |  ||       | ||   ||| |    |  | |   | || ||  |  ||||||||| |  | ||      
AATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTATGTTCCGAGGAAGCCTCGAAAATCACTTGTTTCGAAgtacgc-tccgttctttttgctttgccaaatgattacta-----atttaagcctttttagcttagcccgaatcaagatggacttgtttctctattcattgaatgcg

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|58680150|gb|CK068837.1|CK068837
EST:     TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATCCTGGGCTACTAGGATGTCGGTTGCATTAGGGG
genomic: TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG
EST: gi|25799597|gb|CA755558.1|CA755558
EST:     TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG
genomic: TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG
EST: gi|5443728|gb|D22444.2|D22444
EST:     TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATCCTGGGCTACTAGGATGTCGATTGCATTAGGGG
genomic: TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG
EST: gi|88300985|gb|CI592165.1|CI592165
EST:     TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATC
genomic: TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATC
EST: gi|313081121|gb|HO213707.1|HO213707
EST:     ACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATCCTGGGCTACTAGGATGTCGGTTGCATTAGGGG
genomic: ACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG
EST: gi|86831126|gb|CI295603.1|CI295603
EST:     TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAA                         GGACAGCTACTCCACTATCCTGGGCTACTAGGATGTCGATTGCATTAGGGG
genomic: TGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAG

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: 55 (upstream exon), 75 (downstream exon)
Score: 18

AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaagaatcc ... ttcttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAGCTGCCAAAGGGTTAGCTTGCCTCCACAATGCTGAAAGGCCAATTATCTA




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