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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

Basic information

species Arabidopsis thaliana
transcript AT3G01090.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 4
---------gtaagtgctt--cagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
          | | || ||  ||    |      |||     ||   ||||||     | | |    | |    ||  | |       | |  |||     |||| || || || ||  ||||||||||||||||||| ||||| ||||| |||||||| || || || |||||||| ||||| || |||||||||||||| |
gtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattc---cttttccatttgactagGTGATATCTGGTAAACTATATGCTGGCCCTGAAGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 4
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgttt-caaatgataggtta---tagtcgagatctataaattgttt-cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
||   |  ||      |    |  ||| || |   |||  |   |||  ||| ||    |||  ||    || |  ||   |||   |  ||| ||||| || || || || ||||||||||| ||||| || ||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||||||||||
gtttttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 4
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgttt-caaatgataggtt---atagtcgagatctataaattgttt-cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
    ||  ||      |    |  ||| |  |   |||  |   |||  ||| ||    |||  ||    || |  ||   |||      ||| ||||| || || || || ||||||||||| || || || ||||| ||||||||||| ||||| || || ||||| || ||||| || |||||||||||||| |
----gtatttt---ttttgtatcactgtgagactatatcttcttgctcctttacatgcaatattttttcttattatagtattatggtccctttgcagGTGATCTCTGGTAAATTATATGCTGGACCCGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgttt-----cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
|||  |  |||      | |  |  |     ||    |  ||   | | |||  ||    | |||    | || |  ||   | ||||      |||||||| || || ||  |||||||||| ||||| || ||||| ||||| ||||| ||||| || || |||||||| ||||| || ||||||||||||||||
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttc--ttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 4
gtaagtgcttcagccct-caggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataa-attgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
     |  |  |||         |  |   |      ||  ||    ||   | | || |   |  ||        ||| |   ||| | | |||| || || || ||  |||||||||| |||||||| || |||||||||||||| || || || || |||||||| ||||| || || |||||||| ||||
--gtatcatctagcataatttacaattagcgtccttcatggttgcatttacat-atataacttgccatgacacgtttctgtcttattttcttagGTCATATCTGGTAAACTATATGCTGGTCCTGAAGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
gtaagtgcttcagccc---tcaggtatctgaggaatact------ataatta--ggcttgtttcaaa------tgataggttatagtcgag-atctataaattgttt-cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
|||||   |  |       |||   || | | ||  ||       || | ||  | | | ||||  |      || | |     |||  || |||  |  ||| | | ||||| || || || ||  |||||||||| |||||||| ||||| ||||||||||| || || || || |||||| | ||||| || || ||||||||||| |
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------gtaagtgct-tcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                                                  | | |  | | |         ||  |  |  |   || | |||  ||  ||   | | |||  | |  |   |   || |   || |  ||||| || || || || || |||||||| || |||||||||||||||||||||||||| ||  | || |||||||||||||| || ||||| ||||||||||
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttac-ctccttgtgattaataaatcaaggataaa--ctgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 4
----gtaa-gtgcttcagccctcaggtatctgaggaatac-tataattag-gcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
    |||| |   | ||   |  |  |   ||  ||  |  ||||  ||  |  | ||   | | |||  |  | ||     | | | | || |  ||||| || || || ||  | |||||||| |||||||| |||||||||||||||||||| ||  | || || ||||| ||||| || ||||| ||||||||||
gtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgttt---caaatg-ataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
         |  |   |    ||   |   |  | |||  ||  |  | | |       ||  |  ||  | ||     | | | | || |  ||||| || || || || || |||||||| |||||||| |||||||||||||||||||| ||  | || || ||||| ||||| || ||||| ||||||||||
--------gtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcatttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtaa-gtgcttcagccctcaggtatc---tgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataa-------attg----------tttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                    |||  |    ||   |  |  | |    ||||  ||    ||       || |   | ||||| | | || || || || | |||       |||           ||  |||| || || || |  || || || || ||||| || ||||| |||||||| ||||| ||  | ||||||||||| ||||| || ||||||||||||||||
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgat-gataatggttgaaatttctaaggttctaattagtgtcccattttatagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17922 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                             | |||  |  || ||  ||||   |         || ||       | | | |||     ||||| ||||| || ||| | |||||||| || |||||||| || ||||||||||| |||||||| ||||| ||||||||||| |  ||||| ||||| || |
-------------------------gtcagtatatcaggataagttttgtcataggctcgtcattctaagttgtctttctcaatca---cagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ10631 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                                            |   | ||| |    |   || |  || |||        |  |||||||| || ||||| ||| | ||||| || || ||||| ||||| |||||||||||||| ||| | ||||| ||||| ||||| |   | || ||||| || |
--------------------------------------------gtaagcttcga-cattcttttttcctctagaaagccttttcctttcagGTGATCTCGGGAAAGCTTTATGCAGGACCAGAAGTGGATGTATGGAGCTGTGGTGTCATATTGTACGCACTTCTGTGTGGAAGTTTACCTTTTGACGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                                            |   | ||| | |  |   || |  || |||        |  |||||||| || ||||| ||| | ||||| || || ||||| ||||| |||||||||||||| ||| | ||||| ||||| ||||| |   | || ||||| || |
--------------------------------------------gtaagcttcgactt-tcttttttcctctagaaagccttttcctttcagGTGATCTCGGGAAAGCTTTATGCAGGACCAGAAGTGGATGTATGGAGCTGTGGTGTCATATTGTACGCACTTCTGTGTGGAAGTTTACCTTTTGACGACG

upper sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                             | |||  |  || ||  |||||  |         || ||       | | | |||     ||||| ||||| || ||| | |||||||| || |||||||| || ||||||||||| |||||||| ||||| ||||||||||| |  ||||| ||||| || |
-------------------------gtcagtatatcagtataagttttgttataggctcgtcattctaagttgtctttctcaatca---cagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

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|164165042|gb|ES029549.1|ES029549
EST:     AAATTATGCCGCTCCAGAG                         GTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGT
genomic: AAATTATGCCGCTCCAGAGgtaagtgctt ... attgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGT
EST: gi|86059932|gb|DR355689.1|DR355689
EST:     GTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAG                         GTAATTTCAGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGT
genomic: GTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAGgtaagtgctt ... attgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG
                                              ttgtttc  CT-rich tract
                                     atctataaattgttt  TA-rich tract