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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac...

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgctttt--atttgccct---taggtactaaatat-ctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac
|||||||||||||||||||| || || |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||    |||   |||    ||   ||| ||    ||   || |  |  |  || |   | | | ||  ||||| |  | | |||    |||  | ||     
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgat-tattgtactattatcttattaccagatgcttat-----

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatga-----ctgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac
|||||||||||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||||||| ||||||||||||| ||     ||    |   ||    | || | ||   | | || |    || ||| |||   |  |    |    |  |  ||||   |||| |  ||     
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttg-tgtttgatatattaaaac-tcatgatgatgccatgtattcataggatttgttgatctgaatct---

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttattt---gcccttaggtactaaatatctgcttctgtacaacatcacagt------tgtagagtactgtagtttgat-tcaatgattttcatgcaac--------------
|| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| || ||||| ||||||||  | || || ||||| || |||||||||||||||  || |  |||| |||   |    |   ||  ||  |  |  || |||| || |  | | |      |  |    | | |  | |||| | |||| ||   |||   |              
GTTTTTGACCTTGGGGGTGGAACATTTGATGTTAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttttttatgagtcttaataagaagaactta-ttatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtac-taaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac----------------------------
|||||||| |||||||||||||| || ||||||||||||||||| ||||| || ||||| ||||| ||  | ||||| ||||| || ||||||||||||||  ||| | |||||||   |    |   |    ||| |||| |  | ||    |    | || || | |  |     || | |   |  ||||  ||| |                             
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGg--tgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttc--cttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgct-tctgtacaacatcacagttgt---agagtactgtagtttgat-tcaatgattttcatgcaac--------------
|| ||||||||||| ||||| ||||| ||||||||||||||||| ||||| || ||||| ||||||||  | || || ||||| || |||||||||||||||  || |  ||||   ||    |   ||  ||| |  |  | | |  | || ||   | |  |   | |  | | |  | |||| | |||| ||   ||    |              
GTTTTTGACCTTGGGGGTGGAACATTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac--------------
|||||||| |||||||||||||| || ||||||||||||||||| ||||| |||||||| ||||| ||  | || || ||||| || ||||||||||||||  ||| | |||||||   |    |   |  | | ||    |    |   | ||        || | |  | |   |      ||||  |   ||                   
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGg--tgagtacttttatacacatacacacaagaga-atgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcaca--gttg-tagagtactgtagt----ttgattcaatgattttcatgcaac---------------------------------------------------------------
|| ||||| ||||||||||| || || ||||||||| ||||||||||||| ||||| |||||||||||  |  |||| ||||||||||||||  | |||||||  |    | | |   |   | |  |  |    ||    || ||| ||| | || |   ||| ||    | || | |    |  |   | | | |  ||||   |                                                               
GTGTTTGATCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgat--tcaatgattttcatgcaac-
|| ||||||||||||||||| || || ||||||||| ||||||||||||| ||||| |||||||||||  |  |||| ||||||||||||||  | |||||||  | | ||| |     |   |   |  |    |  ||| |    |    ||      || |  | | ||| |||  ||    |||||||    ||| |  
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaa-tacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgtt-ctgaattgcattgt-gttcaataacaaatgattgctgtgccaat

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgccctta----ggtactaaatatctgcttctgtacaacatca----cagttgtagagtactgtagtttgattcaatgattttcatgcaac
|| ||||| ||||||||||| ||||| ||||||||||||||||| || ||||| ||||| ||||||||  | ||||| ||||| ||||||||||| ||||||| |  |   ||  || | || ||      |  |    || |  | || |  || || |    | |||  ||  | || | || || |  |  ||  |         
GTGTTTGATCTTGGTGGTGGTACATTTGATGTCAGTATCTTGACAATCGACAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagcattgcttccttggtccctaccttatttttgtgcattttttcctttgtaagattagttacggtttaaggattct-tggtgtgttgtagagacctct-------

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgct-tctgtaca---acatcacagttgt-agagtactgtagtttgattc--aatgattttcatgcaac------------
|| ||||||||||||||||| || ||||||||||| |||||||| |||||||| ||||| || |||||  | || || ||||| ||||||||| | ||||||  |  |  |||| | | |   | | |  |  || | |||| | || |||   | |  | | ||   |||| |  ||  ||  | |    ||| |     | |||             
GTTTTTGACCTTGGTGGTGGAACCTTCGATGTCAGCATCTTGACTATTGACAATGGTGTTTTCGAGGTTCTTGCTACAAATGGAGACACTCATTTGGGAGgtgaggatttttttctctactgat-gctctttcatctttgctctttgcacattgaaagaaaatttacgagaggaaagttattatactgtggatgctcaaggttcaattctttcctgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac
|| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |||||||| |||||| | ||||| || ||||| |||||||||||||      |||| ||                ||   || || || | |    | |||| |  | | |    |      || ||                
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgta------ctttgatc---------------aaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcag---------------

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac
|| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |||||||| |||||| | ||||| || ||||| |||||||||||||      |||| ||                ||   || || || | |    | |||| |  | | ||   |      || ||                
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgta------ctttgatc---------------aaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcag---------------

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|58676411|gb|CK065098.1|CK065098
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|29640637|gb|CB645646.1|CB645646
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|86826293|gb|CI311115.1|CI311115
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|58672968|gb|CK061654.1|CK061654
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|29628132|gb|CB633143.1|CB633143
EST:     CAACGGTGTTTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|396941184|gb|HO188393.1|HO188393
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGT
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGT
EST: gi|29628408|gb|CB633419.1|CB633419
EST:     CAACGGTGTTTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|58669929|gb|CK058615.1|CK058615
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|88432555|gb|CI567594.1|CI567594
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|33793958|gb|CF322867.1|CF322867
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|86904389|gb|CI308599.1|CI308599
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCGAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|29631218|gb|CB636227.1|CB636227
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGG
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGG
EST: gi|86851105|gb|CI311323.1|CI311323
EST:     CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|87009611|gb|CI309132.1|CI309132
EST:     AATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: AATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGA

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), 75 (downstream exon)
Score: 257

GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgc ... atctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG