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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g49430.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 2
gtaagc---ttaactactgataatccc-caattccccaagaaccta-cttgaccaccattaaacacat---agttctgttgatttatcaattaacatggaattctagcttattctc-tgataa----------atcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
|||||    |||| || |   || | | || | ||     || ||| |  |||     ||  |    |   | |  ||| |  | |||  ||  |||||   || || ||||| |    ||||          ||  ||||||  ||  ||||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || || |||||||| |||||||| ||
gtaagtatattaattagtaccaaccacacagtacctatccaatctagcaagacagtttttgtatttgtcaaattgttgtgggctcatctgtt--catggttatccagtttattattacaataatgtgatctttatgttctataccggtgcagCTAATGTATTTCATCGTGACCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGTCTTGCCCGTGCATCATTTAA

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
-------------gtaagcttaactac-tgataatc-cccaattccccaaga----------acctacttgaccaccattaaacacatagttctgttgattta-tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
              ||     ||| || || ||     || ||   |||||           |  |    |||     |    ||  |  |  || | || || |   ||   |||  ||  ||   || | |           ||||||||||  ||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || ||||||||||| |||||||||||
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
                                  | ||  ||  |      ||  ||  | |  |   | |    | || |||     |    || | | |  |    || |      |   |  ||    |||||||||||||||||||||||| ||||| |||||| || |||||||| | || |||||  ||||||| |||||||| |||||||| || |   | |||| 
--------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtt-tggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
              | | ||  | ||  |   ||| |  ||  | |       |         | ||||||   ||| |         |||| |  |  | | |||            | |    | |  |||||||||| ||||||||||| || ||||| |||||  |  |||||||| | ||||| ||| ||||||| ||||| || |||||||| ||||   | || | 
--------------tcacaactctca-ctgtacaaaagactgatgggatgtggtcctttttggatttctgtctgttttt--------gtgga-tgttgacgtcttca---------tgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG

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|33795692|gb|CF323716.1|CF323716
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58687543|gb|CK076230.1|CK076230
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     AGTTTTTCCTGTACCAACGTTCGTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: AGTTTTTCCTGTACCAAC-TTC-TCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|66913253|gb|CX100101.1|CX100101
EST:     CCAGGTGTTCCTGTACCAACTTCTTCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|33675107|gb|CF303346.1|CF303346
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|33675390|gb|CF303629.1|CF303629
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58668784|gb|CK057470.1|CK057470
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG

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: 60 (upstream exon), 52 (downstream exon)
Score: 27

GATCTCCATCAAGTCATCAGAGCGAACGATGACCTCACCCCGGAGCACTACCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
                                ataaatcatctatatt  TA-rich tract