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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT

Basic information

species Arabidopsis thaliana
transcript AT2G37270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 3'ss of exon 2
gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCT------TTCCTCTAAG---TTTGCATTATATCAAAGAGTTTTT----------------------------------
                       | | | |   ||||    ||  ||||||  |  |   | | |||||               ||| || ||||||||||||||||||||| |||||||| ||| | ||||| |||||||| |||| || | |   ||       ||   ||||     ||||  | | |   ||   | |                                   
----------------------ctttttgttcggatgataccaggttattgacacatctgtgatctaat---------------tgtgtttcagctatgccatcaagaagaaggatgagatcgagcgtgttgccaagGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGCTAAAGCTCTTGCGCTGTTTGGCAGGACTATACTTTTTGCTAGTAATTTAAGCCTTTTCAGACCTA

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 3'ss of exon 3
gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCT-CCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT
              |  |  | |  | ||  ||||||   | |   || ||  |  |   |   |||||          |||  | | || ||||||||||||||||||||| |||||||||||| | ||||| ||||| || |||| || | |   ||| |  |  |  | | |   |||  |   |   | | 
-------------gtaaatcttgcttctcatttgatgaaatgaggctactgacacatccatgctctaat----------tctgatatgttacagCTATGCCATCAAGAAGAAGGATGAGATTGAGCGTGTTGCCAAGGCGAACCGTTGAGTGCTGAACCCATCTCAGTGTGCTCGAGCTATTGCCTTGCACTGT-

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 3
gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctc-ttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATC-TCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT
    | |||    ||   ||| ||   |||  || |   ||   |    || ||    ||||   | | |      |  |||  |||| || ||||||||||||||||||||| |||||||| ||| | ||||| |||||||| |||| || | |  |||| |  |  |  | |     | |  |   |  |    
----gtacaacacattgtcatggtacatct--tgct--ttttgttcggatgataccaggtta--ttgacacatctgtgatctaattgtgtttcagCTATGCCATCAAGAAGAAGGATGAGATCGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGCTAAAGCTCTTGCGCTGTTTGGC-

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 3
gtaagaacactctatctacatagtctgtctcttgatggcttcactttat-tgtta-gttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAG-GGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT
|||   | |  || |||     | || | | | | ||  ||     ||| ||  | || | ||  ||| ||  |     |   |||||||   |||||| |||||||||||||| || ||||||||| | ||||| |||||||| |||| || ||| ||    | |   |    ||||| || | | | |  | |  
gtatatatatcctgtct-----ggctatatttggttgtttttttcctatctgcgatgtgaattgtgctcat--tcatggcaattcttgtc--acagCTACGCCATCAAGAAGAAGGACGAGATTGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGAGCTTGTATCCTGGTGCACTTGCACTAGAACTACGTTTCTG-

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G156673_T03 (Zea mays), 3'ss of exon 2
gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT---
|||   |   |   | |        ||||| |   ||  | | |   || || |  | |||   || ||  | |   |   ||||||  | ||| || |||||||||||||| || ||||||||| | ||||| |||||||| |||| |   |     |||   ||   ||   |  |       | | ||||    
gtacatatgttgcctgtttgcttcttgtctatctgtgattccgcacgat-gtgaaattgtt---ctcat--tcgtgccaattcttgt--tacagTTACGCCATCAAGAAGAAGGACGAGATTGAGCGTGTTGCCAAGGCCAACCGTTGA---ACTGAGCTTGTATCCTGGTGCACTCTGCGCTGGAAACTTTTATGT

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G37610.1 (Glycine max), 3'ss of exon 4
----------------------gta-agaacactctatct-acatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT-----
                      ||  || | ||  | ||| |  || | | |||  |      |||| |||  |  | |    ||  | | |    |  ||  |      | |  ||||||||| |||||||| || ||||| |||||||||||||| ||||||||||||| ||   |     |     | |  |||||   ||    |||| ||| |     
gtatacttctaaaattttatatgtggaggatacagtttctgatgtattttatcttctatgtctttcatttttctaattggagtttgggttcactgaaaaataatactccattt--cagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCAAAGGCCAATCGTTGAGCAGTTG---TGGAAGCAATATTTGCG--ATCGGGAAGATTTTGTTTCGG

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
---------------------gtaagaacactctatctacatagtctgtct-cttgatggcttcactttattgttagt--tagttaagctaa--taatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT----
                     ||     || | | |  |  || | | | | ||| ||  |||   ||| || ||| |  |  ||  | |    ||     |  |  |  |   || ||||||||| |||||||| || ||||| |||||||||||||| ||||| || |||| ||     |       |  ||  |||||   ||    |||| ||| |    
gtatacttctaggaattctatgtggaggcattttctg-atgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATA--TTTGCG--ATTGTGAAGATTTTGTTTTG

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagaacactctatctacatagtct-gtctc--ttg---atggcttcactttattgtta-gttagttaagct-------aataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT--------
|||| |    |    | || | || | ||||   ||    ||||| ||| | | || | |     ||||  ||       | | |||  |  || |    | || |||||| |||||||||||||| |||||||| ||| | || || ||||||||||||||||        ||     | |  | |  |||  |||   ||  | ||        
gtaaaatgcttgagacaaccttgttttgtctgaattacatatggcgtcattctgttttgatacctgttacacttctctggactgataaaaggttgttgcttgttccagCTACGCCATCAAGAAGAAGGATGAGATCGAGCGTGTGGCCAAGGCCAATCGTTAAG--------CTAGTTGCAAGATGTTTATTGCATCTGGGAACTCTTTAAATGTT

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT-
                          ||  || |  |||   |  || ||  |      | |||||   ||   | |  | | |  | || ||||||||| |||||||| || |||||||||||| | ||||| ||||| ||||||| ||  | | |  | |  | |||     | || |  || |   ||    
--------------------------gtacctcg-cggccagaaattcttcctctcgcctcaagctctaaagttccttgtttttgatgtttcagCTATGCGATCAAGAAAAAGGATGAGATTGAGCGTGTTGCGAAGGCGAATCGTTGAGAAA-CACATTCTAATGTAATGAACCTTTTTGGCATATCATTCGAA

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|86075624|gb|DR371381.1|DR371381
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|301501481|gb|HO207021.1|HO207021
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|164084436|gb|ES116286.1|ES116286
EST:     ATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: ATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|86081297|gb|DR377054.1|DR377054
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT
                       agctaat  putative branch site (score: 3)
                                   catcttctcttgtctt  putative PPT
     tttattgttagtta  TA-rich tract