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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC

Basic information

species Arabidopsis thaliana
transcript AT4G26570.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
-gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
 |||||  |       |   || | || | |      |     || | ||||    | |  | ||  |  | ||        | || |    | |||  | ||||  ||       |||||||||||||||||||||| |||||||| |||| ||| || |||||||| ||| ||| ||||||  |  ||||||| |||||||| || ||||||||||
tgtgtgtgttgagttgataatgat-gacattggtacataaaatcattcttgtgctacta--ttatcttctctgt--------atgtcactgatagttcttgagttattt-------agACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 7
gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
        |     | | |||||  |||   ||  | | ||   | |   |||         |  |||    |        | || |    | |||  ||||||  ||       |||||||||||||||||||||| |||||||| |||| ||| || |||||||| ||| ||| ||||||  |   |||||| |||||||| || ||||||||||
-------actgaatttctctgctaaatatagtaaaccttttgt-cagccttattcttgtgctactataatcttctctgt--atgtcactgatagttcttaagttattt-------agACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTC

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 7
gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgt---atagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttc---tttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
                         ||  | |||  |   |  |   || |   |||   |  || |  |   | |  |   |    || ||||   |  |||| | |  |     |   ||||| || ||||||| ||||||||||||||| |||| ||| || |||||||| ||| ||| ||||||  |   |||||| ||||||||||| ||||||||||
-----------------------aaattatgtatgttgacttgaagattatgccatacaaagttctttgtgctattataatcttctctatagagctatcactaactgtacttaaactcttcagACTTTCGAGGAAGTTGATACAAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCAGCATCCATCCCTTCTAAAAAATATGACTC

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
gtgtggttcc--ttcctaccctgctcgatactatattcttgt--tccac-tgttgtatagccaactcatgatagcagttgagaa--taaagtaaagagt---ggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
|| |    ||  || |||       |  | |||  ||||  |  | ||| ||     ||     |||||  |  |  ||   ||  | |  |  | |||       |  || |||    ||    |||| || |||||||| |||||||| ||||| || | ||| || |||||||||||||||| ||||||| |  | ||||| || ||| | ||||| ||||| |
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 6
gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
          |    |      | ||    ||||| ||      |      |||   | ||    |||  || |    || |  |    | |   |||| | |||  | |    ||||| ||||||||||||||||| |||||||| |||| ||| || |||||||| ||| ||| ||||||| |  | ||||| || ||| | ||||||||||| |
--------gatattgattggattggaatgaatatttttagcattccaa-acatatttatcttgcaata--agcttcctattatatttttaata--ttcttatttttattt----cagACCTTTGAGGAAGCTGATACTAAACATGATGGGAAGATAGACAAGGAAGAATGGCGAAGCCTTGTTTTGCGACATCCATCTCTTTTGAAGAATATGACCC

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 6
--gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
     |||||       |   ||   || |||  |||    ||      ||||     | |    | ||| |  ||                 |  | | |  ||   || || ||  ||| |||||||||||||| ||||||||||| || | ||| || || ||||||||||||| |||||||||  | || || |||||| | |||||||||||||
ctccttggttaagcagcaagttgagggaaactcaatttggattttgtatttgttgcatccatctcttataaccttt-----------------ttttattttggtgcattgttcca--gACCTTTGAGGAAGCTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTC

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|125010993|gb|EL083262.1|EL083262
EST:     ATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAG                         ACATTTGAGGAAGCTGATACAAAAC
genomic: ATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAGgtgtggttcc ... tctttcacagACATTTGAGGAAGCTGATACAAAAC
EST: gi|86076567|gb|DR372324.1|DR372324
EST:     AGTCCGGCATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAG                         ACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAG
genomic: AGTCCGGCATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAGgtgtggttcc ... tctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAG
EST: gi|125286970|gb|EL301055.1|EL301055
EST:     TGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAG                         ACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAG
genomic: TGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAGgtgtggttcc ... tctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAG
EST: gi|125031016|gb|EL103285.1|EL103285
EST:     AGTCCGGCATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAG                         ACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATA
genomic: AGTCCGGCATGAACCTGTCAGACGAAATCATAGAGAGTATAATCGACAAGgtgtggttcc ... tctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC
                                        tttcttctttcac  CT-rich tract
               aataaagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA