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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 4
----TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactctactagcaccactttttttgtatgtagcaaattgt-tgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcag
    | ||||||||||||||||| |||||||| |||||||| |||||||| ||||||||||||| |||||| | |||  |  |       | ||    |   || |      || |||||   || |    |   |  |          |   | |||| |    |   |  |||  || || |  || ||||| ||||  | ||||| | |      | |||||                                   
ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgcaataacttgtgactg------actttgatatgtacta-----ttatgtagccgcctgtggtgttgctttccacggcgctgcacatgttttagatcttcatatcttgcgtgctata-aatcacctt-tcttaatcagatgccatttcacctgttcatag---------------------------------

upper sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 4
----TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactct-actagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcag
    | ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||| ||   |  ||  |||| ||| |                || | ||||| || |   ||   || | |  |||||||    |  | || || ||     || | |  |   | |    | | | |||| |         | |||     ||| ||   | | |  ||  |||||   |  ||   ||
ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgcaacaactcctgacttagatatgttttat---------------tatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtccttt-ttgtaa-------tcagatg-----catctcctaatttgcaatgccatttgacctgttcatag
















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|5003279|gb|AU068428.1|AU068428
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|86596734|gb|CI286647.1|CI286647
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58654229|gb|CK042909.1|CK042909
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58652484|gb|CK041164.1|CK041164
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29618976|gb|CB623988.1|CB623988
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     CATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCANG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCA
genomic: CATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCA-Ggttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCA
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|2317492|gb|C22546.1|C22546
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAG
EST: gi|58653056|gb|CK041736.1|CK041736
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     ACATGCCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58657986|gb|CK046666.1|CK046666
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
EST: gi|58673516|gb|CK062202.1|CK062202
EST:     ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG                         GCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAG

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), 75 (downstream exon)
Score: 62

TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgca ... ccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC




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