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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaacctattcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag

Basic information

species Arabidopsis thaliana
transcript AT1G30230.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgt---ttcatgaacct----attcgtaattcttttta--agctgtgatctt-ttgttaga-taatgtggt-gtgtaactgtctatgttggattgaatcataatgcaggag
    |||| ||  |||| |   |||| || ||  |  ||      |||||    ||||| ||  |||||||||| ||||||||||| ||||||||||| |||||||   | ||| |   |       |||  || | |||   |||  || |||| || ||| | | | |   | |  | ||   || | ||   || |               
GATCTTGTGTCGGTTGATAGTCTGATTGAGGACTACTTCTACACCGAACCAGCGAATGAGTACATCCAGAGCTGCGACATTGTTGCGTTCAACAAGATCTgtaagttattccataagtatcagagcccgtcgttttatttgctagcgttgttcttgttattatactgaagcaatcggatgaccagctgtcttattttaag--------------

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaacctattcgtaattctttttaagctgtgatcttttgttagat-aatgtggtg-tgtaactgtctatgttggattgaatcataatgcaggag--
    |||| ||| | ||||   | || || ||  |  |       |||||    ||||| | | | ||||| |||||||||||||| |||||||| || |||||||| | ||     |    |  | |||||  || |  ||| |     ||  | ||  |  || | | | ||  ||||    | |  |   || || |  |   
GATCTTGTTTCTGTGGACAGTCTCATTGAGGATTATTTTTACACGGAACCAGCTAATGAGTTTATTCAGAGTTGTGACATTGTTGCTTTCAACAAAATCTgtaagttccttgg---caagtttggtgctttt--agtttggatttccaaataactgaaactaatggtttgattgaatatgcaaaactctaat-tagtgtaataaaa

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgt--ttcatgaacctattcgtaattctttttaagctgtgatcttttgttagataatgtggt--gtgtaactgtctatgttg-gattgaatcataatgcaggag-------------------------------------------------------------------
    |||||||| |||||||  | ||||| || || |||   | ||| ||  | |  ||||| ||||||||||| |||||||| |||||||||||||| |||||||  ||||| |    || | ||   ||     |||  | | ||      |   ||  |  |   | ||   |||| |  ||  |   | |||| || | ||                                                                     
GACCTTGTCTCTGTTGACACTCTCATCGAGGACCATCTCTGCGCTGAGCCAGTGAGCGAATACGTCCAGAGCTGCGACATTGTCGCCTTCAACAAGATCTgtaagtcattcatcacttaatccttacagctgcagtagc-ataa-ctaggaccatgcaacctactcattatattggtctgtcatgcaacctactcattatactgggttgtccagttgtaaacttttctgctctcaatgtgttgataacttttggtcaatcctgttgtgttgcag

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G031545_T02 (Zea mays), 5'ss of exon 7
TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaaccta---ttcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgtctatgttggattg--aatcataatgcaggag
|||||||| | |||||  | || || ||  | ||    | ||| ||  | || || || || |||||||| ||||| ||||||||||||||||| |||||||  |   |  ||      | ||   ||     |||  |  |     |||   | |  ||     ||  |  |  |||    ||    ||  | |  ||    
TTGTCTCTGTCGACACTCTCATTGAGGACTATCTGTGCGCTGAGCCAGTGAACGAGTACGTGCAGAGCTGCGACATAGTTGCCTTCAACAAGATCTGTAAgtcactcaactcttgaccccttacagctgcagtagcattactaggccgttgctttaactgcccattacattgccgtgtccagtttgtgatttttactcaa---

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G031545_T01 (Zea mays), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtt-------tcatgaacctat----tcgtaat--tctttttaagctgtgatctt--ttgttag--ataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag---------------
    |||||||| | |||||  | || || ||  | ||    | ||| ||  | || || || || |||||||| ||||| ||||||||||||||||| |||||||        || ||| ||  |      | | |    ||  || || ||    ||   ||      | | ||  ||||  |  |    || ||   |  |  | |||  | |                  
GACCTTGTCTCTGTCGACACTCTCATTGAGGACTATCTGTGCGCTGAGCCAGTGAACGAGTACGTGCAGAGCTGCGACATAGTTGCCTTCAACAAGATCTgtaagtcactcaactcttgaccccttacagctgcagtagcattactaggccgttgctttaactgcccattacattgccgtgtccagtttgtgatttttactcaaggc-taacactgacttttctgttggttcag

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA04G37120.2 (Glycine max), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaa---------cctattcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgt-ctatgttggattgaatcataatgcaggag----------------------
    | || ||| |||| ||  | || || || || ||||| ||||| || |||||||||||||||||||| ||||||||||| |||||||| || ||||||||||||  |  |         | ||| | || |  ||  |||| | || | || | || | | |   | |   || |  |  ||| | |  ||| ||| |  |  |  |                       
GACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCTCACAGTTGAGCCCATCAATGAATATGTCCAGAGTTGTGACATTGTGGCCTTCAATAAAATATgtaagttttttagatgaccttttcttatccctagtaattcctaaggt-tggtgttgtatttgttgacaagattcatatccttgttatatggttttgcatcttgttataacacgctatttcatatcttattacag

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G17930.1 (Glycine max), 5'ss of exon 7
TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgt---ttcatgaacctattcgtaattctttttaagctgtga------tcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag--------------------
| || ||| |||| ||  | || || || || ||||| ||||| || |||||||||||||||||||| ||||||||||| |||||||| || ||||||||||   || |     || ||| | || |||  |||    | |      | || | || | |     | |   ||  | | ||| | |  ||| ||| |  |  |                        
TAGTTTCTGTTGATACTCTTATTGAGGAACATCTCACAGTTGAGCCCATCAATGAATATGTCCAGAGTTGTGACATTGTGGCCTTCAATAAAATATGTAAgtatttttagatgacttttctttatccttagtaattcctaaagttggttttgtatttgttggcaagattcatatttttttatatggttttgcatcttgttataacgctacttcataacttgttacag

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G17930.4 (Glycine max), 5'ss of exon 6
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgt---ttcatgaacctattcgtaattctttttaagctgtga------tcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag--------------------
    | || ||| |||| ||  | || || || || ||||| ||||| || |||||||||||||||||||| ||||||||||| |||||||| || ||||||||||   || |     || ||| | || |||  |||    | |      | || | || | |     | |   ||  | | ||| | |  ||| ||| |  |  |                        
GACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCTCACAGTTGAGCCCATCAATGAATATGTCCAGAGTTGTGACATTGTGGCCTTCAATAAAATATgtaagtatttttagatgacttttctttatccttagtaattcctaaagttggttttgtatttgttggcaagattcatatttttttatatggttttgcatcttgttataacgctacttcataacttgttacag

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 5'ss of exon 7
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaacctattcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag
    | || ||| | |||  | | || || || ||  | ||||||||||| |  ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |||   | | ||      | |    |  |    ||| |||| |      |||  | |||  ||                               
GACTTGGTTTCTGTGGACGACCTTATTGAGGAACAGTTGACTGTTGAACCCACGAATGAGTATGTCCAGAGCTGTGACATTGTAGCCTTCAACAAGATATgtaagtt-cattttcatgttgtgtggtatagggatccaaccatcctttgctgtgctctgttctatgtttcttgag---------------------------

upper sequence: AT1G30230.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S145_172V6.1 (Physcomitrella patens), 5'ss of exon 5
----TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaacctat-tcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag-------------------
    | |||  ||| |||| | |||| || || || || ||    || || | ||| || ||  | |||   ||||||||||||||||||||||||||||||||||      |       |  |  |||| |||   || | |  |     || | ||| | |    |   || |    ||  ||       |    |   |                    
GACCTCGTCAGTATCGACAACCTGATTGAGGACCATCTGACCTCCGAGCCCAACAACGAGTACATTCAGTCTTGTGACATTGTTGCCTTCAACAAGATATgtaagtacttcaatttcgggttttttttctcttttctctatcacgtaaaaataaacaatttaggcctttgttggc-gcattaaatctggctgtttcacttaactgtattttcaattttgcag

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|164162998|gb|ES188020.1|ES188020
EST:     ACAAGATATG-AG                         GATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
genomic: ACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
EST: gi|116453708|gb|EG496300.1|EG496300
EST:     AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGGG-                         GATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
genomic: AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
EST: gi|116453709|gb|EG496301.1|EG496301
EST:     AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGGG-                         GATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
genomic: AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
EST: gi|86085521|gb|DR381280.1|DR381280
EST:     AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATG-AG                         GATGGA-AAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
genomic: AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
EST: gi|164064194|gb|ES143261.1|ES143261
EST:     CAACAAGATATG-AG                         GATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
genomic: CAACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTCTGGTTCTTCTT
EST: gi|116416034|gb|EG458626.1|EG458626
EST:     AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATG-AG                         GATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTC
genomic: AATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaa ... aatgcaggagGATGGAGAAAGCTTCAAGGAATGTCTGTGTTCATGTGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCTCTATTGACACCATGATCGAAGAGCAACTCACTGTTGAACCGATCAATGAATATGTCCAGAGCTGTGACATTGTTGCCTTCAACAAGATATGTAAgtttcatgaacctattcgtaattctttttaagctgtgatcttttgttagataatgtggtgtgtaactgtctatgttggattgaatcataatgcaggag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT