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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC

Basic information

species Arabidopsis thaliana
transcript AT4G38600.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                                                                                                               | | || |      ||   | || |  |  | ||       || ||  ||    ||||  | |  |  ||  || | || ||| ||||||| ||||| || ||||| | |||||| |||||||||||||| |||| ||| |||||||| || ||  | || || || |||||  
gtaatcactctctgcctattatagacttttgcatcacaaaatactttgtttgtttcagctcatttatctcatagcttattcttatgcattacttgtcattatattgtgacagatgaactgtattatttattcttgttatttatttttattactaactgttgtttttgttgatggaatgttttcagAGAGTTGCATTATCTACAGCTGCTAATATGTGTAGGAAACTTCCTTCTGATGCATCAGATTTTGTAATGGAAGCGGTTCCACTTCTTACTAATCTACTGA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttact---cgtgtatcta-atgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                                                        ||| ||    |  | | | |       | | |  ||| |   |  || | |  |||   |  ||| |    || ||  |||| || ||| | ||||||||||| || ||||||||||| || ||||| |||||| |||||| ||| ||||||||||| ||| | ||||||||||| ||||
gtaaattgtcagtgaagtacctaaatttagaggatgattatattatatggtccttttggatagtcataaatcatttggccacagatgcctttagtgagcaagtgtgtgtatgttgacattattc--tttgtttcagCGGGTTGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTTCAGATGCAGCTGATTTTGTGATGGAAGCTGTTCCTCTTCTGACAAACCTTCTTC

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                                                         |||  |    |  | | | |       | | |  ||| |     |    |||   |  ||| |    || ||  |||| || ||| | ||||||||||| || |||||||| || || ||||| |||||| |||||| ||| ||||||||||| ||| | ||||||||||| ||||
gtaaattgtcagtgaagtacctacatttagaggatgattgcatcccactggtccttttggacagtcataaatcatttggccacaggtgccattagtgagcaagtgtatgttgacattattc--tttgtttcagCGGGTTGCATTGTCTACTGCTGCAAATATGTGCAAAAAGCTTCCTTCAGATGCAGCTGATTTTGTGATGGAAGCTGTTCCTCTTCTGACAAACCTTCTTC

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 2
-------gtgggtaaatttctaacttc---------tcttttatgctacactt---actcgtgtatctaatgcacatgtt-acttggct-tcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
        |   | || | ||||  ||         |  || ||  | || ||   || | ||  |   | ||  || || ||       | ||  |||| || ||| | ||||||||||| || ||||||||||| || ||| |||||||| |||| | ||| ||||||||||| ||  |  |||||||||| ||||
gtaactcatcaatgaaatcctaatatcaaagggtgatgattcattttgcatttgccacccttgattggcaagcctatattgacacaatcatgtttcagCGGGTGGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTCCTGATGCAGCTGACTTTGTGATGGAAGCTGTTCCACTTTTGACAAACCTCCTTC

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 2
-------gtgggtaaatttctaacttc---------tcttttatgctacacttact---cgtgtatctaatgcacatgtt-acttggct---tcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
        |   | || | ||||| ||            || ||  | |  ||||    | ||  |   | ||  || || || |       | ||  |||| || ||| | ||||||||||| || ||||||||||| || ||| |||||||| |||| | ||| ||||||||||| ||  |  |||||||||| ||||
gtaactaatcaatgaaatcctaacatcaaagggtgacaattcattttgcgtttaccacccttgattagcaagcctatattgacataatcatgtgtttcagCGGGTGGCATTGTCTACTGCTGCAAATATGTGCAAGAAGCTTCCTCCTGATGCAGCTGACTTTGTGATGGAAGCTGTTCCACTTTTGACAAACCTCCTTC

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                                                                | ||| | | | ||   || | |||| ||       |  ||  |||  | || | | | |||||    || ||  |||| || ||  | ||||| ||||| || |||||||||||||| ||||| |||||| |||| | ||| ||||||||||| ||| || |||| ||||| || |
gtaaatcgccattaaaatttgtgtgtgtatattctttttaacctttttgttgattatgcacgctgagggaagaatactgttttatattttgtg----gggtcatcaagtaatttat-ctccttttact--atttgtttcagCGAGTGGCCTTGTCTACAGCTGCAAATATGTGCAAGAAACTCCCTTCAGATGCAGCTGACTTTGTGATGGAAGCTGTCCCTCTGTTGACGAACCTTCTGC

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                      |||   |     | |   | || ||   | | || | |  | | |       |  ||| ||   |  ||  || | |||||| | || ||||||||||| ||||| |||||||| ||| | |||||| | || | ||| ||||||||||| ||| |  |||||||||| ||||
gtaaaattttggctatttactcgtatgctgtgctccttggtcttctggggc-catattgggatttttctgaagaagtttatttccatgttttcagAGAGTAGCATTGTCCACTGCTGCCAATATGTGTAAGAAACTCCCTCCAGATGCAGCCGACTTTGTGATGGAAGCTGTGCCTCTTTTGACAAACCTTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC
                                             cttcttgt  CT-rich tract
                      tatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtaaatttctaacttctcttttatgctacacttactcgtgtatctaatgcacatgttacttggcttcttgtagCGCGTAGCACTATCTACTGCTGCCAACATGTGCAAGAAACTACCTTCTGATGCATCTGATTATGTTATGGAAGCTGTACCTTTGCTGACAAACCTACTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG