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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA

Basic information

species Oryza sativa
transcript LOC_Os11g48030.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059282_T01 (Zea mays), 3'ss of exon 1
gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
||  |   |  | | | |||  |  ||| ||  ||    | | |||  | |  |               |||| |     |   | |  ||||||||||||||| ||||||||| ||||||||||  | ||||| ||||||  ||||  |||||||||||||||||||||||| ||||| ||||||||||| ||
gtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcaca---------------tccatccctctcgtcttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G000623_T02 (Zea mays), 3'ss of exon 1
gttcgtctccttcc-ccatctatcgatccgattcgctttgctttctcaaaccctagattgccttg-aattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
||  ||  |||||   | |  |||  | |  |||  |     ||| |   ||    ||  | |   ||    || ||   ||   ||||    ||||||| ||||||||||||||| ||||||||||| | ||||| ||||||  ||||   ||||||||||||||||||||||||||||| ||||||||||| ||
gtaggtacccttcaatccttcatctcttccgttcatt---agttcgccgtcctcgcatcacatcacaaccgcccccctcgtc---atcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G41410.1 (Glycine max), 3'ss of exon 1
gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattat--ccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
||||||     |     | |||         |  |     ||||||      |||  | ||  |  | |     |  | |   |  ||    | |||  | ||| | |||| ||   | ||||| ||||  || || |||||||||||| |||| ||||||||||| ||||||||||| || |||   ||||| | 
gttcgttattatat---tttattatattatattacccccttttctctgcaattagggttccaagtttcaaaattataataataatttctttgatagGGAGTTTCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATT

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G03990.1 (Glycine max), 3'ss of exon 1
gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
|||||  | ||      |   |  ||||  ||  |  || |   |      | |  || |       ||   |  | |   |  ||    | |||  | ||| | |||| ||   | ||||| ||||  || || |||||||||||| |||| ||||||||||| ||||||||||| || |||   ||||| | 
gttcga-tactagtattttattttatccccttttcactg-taattagggttccaagtttcaaaactataataataataataatttctttgatagGGAGTTTCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATT

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G59140.1 (Arabidopsis thaliana), 3'ss of exon 1
---gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacac---agGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
    || |  |       ||  |    || |         | ||   |   |   |  |    ||  | |||   |     |    ||     |    ||| || ||||| ||  ||   || ||||  || |  ||||| || || |||||| | || || |||||||| |||||||||||||||||||| || || ||
gtaatttgaataaagaagcaagtccaaattcataagatcattctcaatttcattatgtagatgctaaatttagtaattctgttgttatttggtatggtagGTGGTTTCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATA

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 3'ss of exon 1
----------gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
           || || |  ||  |    | ||  |   |  |     | | | |  ||     || ||  ||    |  | |     |     ||     ||||  ||||  | || | |    | || || || |  ||||| ||||| |||||| |||| || ||||||||||||||||| ||||||||||| || || | 
tatatgaaattttggtttatttgtcttaatttcctttgcaaccaaacggttgtttggaatttgggagtgagtt---ctgactag-gttttttggtcggcttcagGGAGCTTTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATT

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO98353 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------------------------------------------------------------------------------------------gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgcct-tgaattatccaccaaatccaaat---------ccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
                                                                                                 |  |   |  |  | |      |      || |   |||  | | ||  |  |  |  |       |    |||   ||||             ||  | ||||  ||||| | ||||||     ||||||||| | |||||| ||||||  ||| |||||||| |||||| ||||||||||||| ||||     || | |||
gtgacgccacgctcaccctcagtttacggggcgcagtcacgtaggcttcatagtatttggggcgtcggagaggtccagtgtgacctgaagaatggcctgggctgcggtatcaacacgcgggcgttgttggagctgcaatgtgaacgcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ27116 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
                                    | ||  ||   |     |     |    ||||   | |  |         |     |||  ||||  |||||||      ||| ||||| || || || ||||||||||| || || ||||||||  | ||||||||||||||||||||  | || | 
-----------------------------------gtagccctcgggagattca-----ctgaaaattcctctctgagattctcggcgttctagGGAGCTTTACCGAGACCGAATTGGGAGAGGTCAGATTTCCAGAGATCAGCACGCCGATTCTCGAGAAAGTGTGCCAGTACTTCTACTGGTCATTGCAATT

upper sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21515 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
                                    | ||  ||   |     |     |    ||||   | |  |         ||    |||  ||||  |||||||      ||| ||||| || || || ||||||||||| || || ||||||||  | ||||||||||||||||||||  | || | 
-----------------------------------gtagccctcgggagattca-----ctgaaaattcctctctgagattctcggcattctagGGAGCTTTACCGAGACCGAATTGGGAGAGGTGAGATTTCCAGAGATCAGCACGCCGATTCTCGAGAAAGTGTGCCAGTACTTCTACTGGTCATTGCAATT

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|86413185|gb|CI067590.1|CI067590
EST:     GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCG                         GCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
genomic: GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
EST: gi|88211322|gb|CI210962.1|CI210962
EST:     GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCG                         GCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
genomic: GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
EST: gi|88208303|gb|CI208152.1|CI208152
EST:     GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCG                         GCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
genomic: GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
EST: gi|88550027|gb|CI479967.1|CI479967
EST:     GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCG                         GCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
genomic: GAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
EST: gi|88476473|gb|CI413744.1|CI413744
EST:     GCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCG                         GCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA
genomic: GCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCA

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: 67 (upstream exon), 68 (downstream exon)
Score: 47

GGCTTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAGTTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctcc ... tccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
                      ttgaattat  TA-rich tract