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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtactggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG

Basic information

species Arabidopsis thaliana
transcript AT4G30890.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G327635_T01 (Zea mays), 3'ss of exon 3
--gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtactggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTC-TAAG
       |   |   | |     |  | |  ||| ||  |    ||   | || | ||    |  |  |    || |||  |     |    |  ||| ||||||||||||||||||||||||||| ||||||   |||||   | ||||||||||  || |||| || || |   | |       | |||  |     || |
ttacattttgtttgttaatgtccttcacaaattgttgtctatcttgcaatgaagattttg-gttcagtttgtgatgctatatgcacttttgcgctctg-cagGCAGGAAGATGCTCAAGAGTTTTTAAGTTTTGCCATGGATAGAGTGCATGATGAACTGCTGAAGCTTAATGG-TAATGGTTTGGATTCAAAGGAGGGTATG

upper sequence: AT4G30890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G330690_T02 (Zea mays), 3'ss of exon 3
gttagtgactcccttac-acagtctaaattttgatggttcctctgtt-ttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtactg-gcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG-
 ||      | | || | |  ||||    |||   | |  |||  ||  ||   || |  |   |  ||   |  |    || ||      ||| ||  |||||||||||||||||||||||||||| ||||||   |||||   ||||||||||||  || ||||||| || | | | |      || |||  |      |  
ttttacattttctttgctaatgtcttttctttatcgttgtctcccttgctatgaagcttttggtttagtttgtgatt---ctatgcacttttgtgctctgcagGCAGGAAGATGCTCAAGAGTTTTTAAGTTTTGCCATGGATAGAATGCATGATGAACTGCTGAAACTTAATGGAGA-TGGTTTGAATTCAAAGGAGGGGATG

upper sequence: AT4G30890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G35900.1 (Glycine max), 3'ss of exon 3
gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattcta-actttgtgt--gcatgt-actggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG
 || || | |   | | |  ||  ||      |  ||     | |  |   ||    | |  |    |  | |  || |||| || |   ||||| |||  ||| |||||||||||||| || ||| |||| ||| ||||||| |||||||||||||| ||  |||| ||  | | ||| ||  | |   | | ||     || 
-ttggtaatt---tgaaagtgtggaatgcccaagtgtcatgatctaattggtaacataaacttgcaactttgtaatatacttggtttcaacatgtcactttcagACAGGAAGATGCTCAGGAATTTCTGAGCTTTGTAATGGATCAAATGCATGATGAATTACTGAAGCTTGAAGGACACTCTTCAAGTCTTAACGGCAGCAAA

upper sequence: AT4G30890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G01430.1 (Glycine max), 3'ss of exon 3
gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattcta-actttgtgt--gcatgt-actggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG
 || || | |   | | |  ||  ||    | |  ||     |||  |   ||    | |  |       | |  || | || ||||   ||||| |||  ||| |||||||||||||| || ||| |||| ||| ||||||| |||||||||||||| ||  |||| ||  | | ||||||  | |   | |  | |   || 
-ttggtaatt---tgaaagtgtggaatgcctaagtgtcatgatgtaattggtaacataaacttgcaattttgtaatatagttagtgtcaacatgtcactttcagACAGGAAGATGCTCAGGAATTTCTGAGCTTTGTAATGGATCAAATGCATGATGAATTACTGAAGCTTGAAGGACAGTCTTCAAGTCTTAATGGTAGCAAA

upper sequence: AT4G30890.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g01690.t01 (Vitis vinifera), 3'ss of exon 3
gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtac-----tggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG
     | | |     ||| | | |   | || ||  |||      | |||| | |   | ||  |||        |  | ||||   |||   |     |  |||||||||||||||||| |||||||| || ||| | ||||| |||||||| ||||| ||  | |||||  | |     |   | ||  | |  |     || 
----tttattaggcaacaaaatatccttatt-atcattcaaaacatctaaaaaatgattgtggttgtattggaatttgcattgtaaacattctcaaccttttcagGCAGGAAGATGCTCAGGAGTTTTTAAGCTTTGTCATGGATCAAATGCACGATGAATTACTTAAACTTGAAGGGTTCTTTTCAAATTTAAATGGGGGGAAA

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|164085039|gb|EL988410.1|EL988410
EST:     ATTTTACCCCAGATGTACTCAACAACATGTCTGGTAGGCCAAG                         GCAGGAAGATGCTCAAGAGTTTTTTGAGTTTTATAATGGACCAAATGCATG
genomic: ATTTTACCCCAGATGTACTCAACAACATGTCTGGTAGGCCAAGgttagtgact ... gtactggcagGCAGGAAGATGCTCAAGAGTTTTT-GAGTTTTATAATGGACCAAATGCATG
EST: gi|164211694|gb|EL988989.1|EL988989
EST:     ATTTTACCCCAGATGTACTCAACAACATGTCTGGTAGGCCAAG                         GCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGA
genomic: ATTTTACCCCAGATGTACTCAACAACATGTCTGGTAGGCCAAGgttagtgact ... gtactggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtactggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG
                           ttctaac  putative branch site (score: 1)
            atatgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgactcccttacacagtctaaattttgatggttcctctgttttaaatagttcatatgtatgtccctattctaactttgtgtgcatgtactggcagGCAGGAAGATGCTCAAGAGTTTTTGAGTTTTATAATGGACCAAATGCATGATGAGTTGTTGAAACTCAAGGAACAGTCCCCCAAAGTCACCGCTTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA