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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC

Basic information

species Oryza sativa
transcript LOC_Os02g04020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
     || |    |||| ||   | | |  | |  |  | ||||  ||| ||||  |  | ||   |     | ||   | | ||||| ||||| ||||||||||||||||||||||||||||| || |||||  ||||||||||||||||||||||||| || || ||||| ||  |||||||||
-----gtatgagcctcattttttttacactctcttttgt-tgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G073571_T03 (Zea mays), 3'ss of exon 5
gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcg--tggttt--tatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
     || |    ||||||||  |  ||  |||  |  ||   |  ||||||||||     | | || |  |  |||    | | | ||||| ||||| ||||||||||| ||||||||||||||||| || ||| |  |||||||||||||||||||||| || || || ||||| ||  |||||||||
-----gtatgagcctcaattcattttta--cactttgttgctgtttttttcttgcttggaatatattgggttaatttgtcgtatctccagACTCTATACCAAATGTTTATCGTCAATGCTGGTCCGGGCTTCCGGTTACTATGGAACACTGTGAAGTCCTTCCTTGATCCCAAAACGACCGCCAAGATAC

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
                                                | ||   ||   |     | ||  ||    |   |  | |  ||   |        ||   |  ||| |   || ||   | ||||| || |  |||||||||||| | |||||||| || || ||| |||| || |||| |||||| ||||| ||||| || || ||||| ||||| ||||| |
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaata-atacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
                                                     | |||  ||   |     | ||  ||  | |   |  | |  ||   |    |   |||  |  ||| |   || |||  | ||||| || |  |||||||||||| | |||||||| || || ||| |||| || ||||||||||| ||||| ||||| || || ||||| ||||| ||||| |
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatg-atacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------------gtactgtcttctactca-attcgctgataag-cacagtactgtg-ttaattttcttgctaacttttttt----tcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
                                                            |  |||    || |   ||| |  | |||  | || | |||   || | | |  | |||     || |    |       | |  | | ||||| || |  |||||||||||  | ||||||||||| || ||| ||||  | |||||||| |||||| | ||||| || |||||||| ||||||||||| |
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC

upper sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
gtactgtcttctactcaattcgc-tgataagc-acagtactgtgttaattt--------tcttgctaact---tttttttcgtgg-----------ttttatgtgtt-cagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
||| |      |  ||  ||  | |||||||| | |||  |     | ||         | | | | |||   | | |  | |||           | |||  || | ||||| || |  |||||||||||| ||||||||||||| || ||| ||||  | ||||||||||| ||| | ||||| || || ||||| ||||||||||| |
gtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctcttaactgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC

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|29625318|gb|CB630329.1|CB630329
EST:     GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
genomic: GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
EST: gi|29625357|gb|CB630368.1|CB630368
EST:     GGGAATTAATTGACCGATTGCAAAAAATTGATAATGATAACTACCCACAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGGCCGGGGTTTCGGCTCTTA
genomic: GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
EST: gi|58659119|gb|CK047799.1|CK047799
EST:     TGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
genomic: TGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
EST: gi|29640359|gb|CB645368.1|CB645368
EST:     GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
genomic: GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
EST: gi|2310407|gb|C26562.1|C26562
EST:     GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
genomic: GTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA
EST: gi|113931032|gb|DQ884125.1|DQ884125
EST:     GTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAG                         ACCCTATATCAAATGTTTATTGTCAATGCTGGTTCGGGGTTTCGGCTCTTA
genomic: GTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTA

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: 73 (upstream exon), 57 (downstream exon)
Score: 45

GGTTTGAAAAATTTCAGCAAAACTGCACGTGAATTAATTGTCCGATTGCAAAAAATTGATAATGATAACTACCCAGAGgtactgtctt ... atgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
                     tgctaac  putative branch site (score: 45)
                        taactttttttt  TA-rich tract