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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG

Basic information

species Oryza sativa
transcript LOC_Os02g54340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 4
gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
|||| |||||||  |   |||||  | |   |||  |    |        ||| |||  | |  |||   || |  | |  || ||| | |||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||||| || ||
gtatgccatgctcgtgtcatttttctcatctcatgccaccta-------gaatttgtgcagcttttt---atgccttgtaatgaatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 4
---gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcatt-----cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
    | |   |||||     || |    |||        |  |  ||||        |||||  ||   | |   | |   || ||  |   |     |||||||| ||||| ||||| || || ||||| || |||||||| |||||||||||| | || ||
gtcttgtcttatgctatgtgaaatgccatgattttcccccccttttgaagttgc-catgttgcacctaatataccattaccttctgctttgatgatggcagTTTGTTGTTGGGCTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtattccatgcttatccaattttattga--aacca--tatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcatt--cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                        | |   || |||    || | | |     | ||  | ||||   |     ||||||    | |   | |   ||||  | |  | |    ||   ||||||| ||||| ||||| || || ||||| || ||||||||||||||||||||| | || ||
gtacctataatttttttaacaatcttttcatctttcccttttctagttgtttgtttgaagatgtttggcttcacttgttgattaagagatatcacttgctgatcagttgtcttatgttttgtaaaatgccaagttgggtctaatataccttctgctttgatgttgatagTTTGTTGTTGGGCTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------gtattcc-atgcttatccaattttattgaaaccatatctttcatgaa--aaaaaatgtgttgatccctttctc-atactgta--------------ttttgtatcatt-------cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                              || |    ||| |   |     ||| ||  |  | ||  |  |||       |||  ||||||| | |||||  || ||||               || ||  |  ||       |||||||| ||||| || || ||||||||||| || || |||||||||||||||||| | || ||
gtaatctatattttcaacaatgtgaagaagatgccaaactgtcccattgtttctcaccacatttatcctatattcttggtttgaagatgttagacttcacttactgttatgaaattgtcaatgggttggcaaagctgttgattcttttctttatgctgtcaggactaataatccttctgcgttctttttatgacagTTTGTCGTTGGGCTGGGTGATAAAGTTTCACCTACCGACATTGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------gtattcca--tgcttatccaattttattgaaaccatatctttcatgaa--aaaaaatgtgttgatccctttctcatactgta--------------ttttgtatcatt-------cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                          || ||  |  || |   |     ||| ||  |  | ||  |  |||       |||  ||||||| | ||  | || ||||               || ||  |  ||       |||||||| ||||| || || || |||||||| || || |||||||||||||||||| | || ||
gtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG

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|58603359|gb|CK013887.1|CK013887
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATCAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|88574346|gb|CI666115.1|CI666115
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCCTCCA-CTGACATTGAGGAA
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTC-TCCAACTGACATTGAGGAA

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: 75 (upstream exon), 72 (downstream exon)
Score: 50

GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                tgttgat  putative branch site (score: 50)
      aaaaaaaatgtgtt  TA-rich tract