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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactataaactttacgctacttctctgcttcatcatgcggccttgtaaattaaaaaatctcgatttctttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG

Basic information

species Arabidopsis thaliana
transcript AT5G48300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 3
---------------------------------gtactataaactttacgctacttctctgcttcatcatgcggccttgtaaattaaaaaatctcgatttctttgctcc------------tagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG
                                  |   ||| | ||   |  | |  | |  |  | | |      ||     ||||||   ||  || || |   ||             ||||||||||| || || || || ||||||||  |||| || ||||| |||||||  |||||||| |||||||| |||||| | ||||  |||||||||||  
gtacacataatttgccttttctttcaagctaacttgacatacatttgttgacaatcatttagtgaacc-taaaatattcccctttaaaatgccttcatctcatatttctgtctgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGAGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATATATGTTTTTAGCAAGGATGTAATGCTTC

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
---------------gtactataaactttacgctacttctctgcttcatcatgcggccttgtaaattaa--aaaatctcgat-ttctttgctc---ctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG
                | ||  ||| ||    |   || |||   |    | |  ||| |  ||||  |   | |||    | || |||| |     ||||||||||| || || || || ||||||||   ||| || ||||| |||||||  |||||||| |||||||| |||||| | |||| ||||||||||||  
ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgttgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtactataaactttacgctacttctctgcttca-tcatgcggcctt---gtaaattaaaaaatct----cgatttcttt--------gctcct----agGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG
                              || | ||  ||||    | | ||| | || || |  ||  |  ||   ||   |||| ||  ||    || |||| ||        | ||||    |||| || || || || || |||||||||||| ||||||| || || ||||||| |||||||||||||||||| ||||| || |||| |||||| ||| |||
gtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaagGTCGATACTACCATCCTGGGTCTTGATGATGAGAGAGCTAAAGAAATGCCTTACATTGCTAGTATGGGTATATATGTCGTCAGCAAAGATGTGATGTTAG

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|124907613|gb|EH981693.1|EH981693
EST:     AAACCAAAAGGGGAGCACCTAAAGGCCATGAAG                         GTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGG
genomic: AAACCAAAAGGGGAGCACCTAAAGGCCATGAAGgtactataaa ... ttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGG
EST: gi|124987384|gb|EL059844.1|EL059844
EST:     TTATTGAATTTGCTG-AAAACCAAAAGGGGAGCACCTAAAGGCCATGAAG                         GTTGACACAACAATTCTAGGTCTTGATGAATCAGAGAGCCAAGGAGATGCC
genomic: TTATTGAATTTGCTGAAAAACCAAAAGGGGAGCACCTAAAGGCCATGAAGgtactataaa ... ttgctcctagGTTGACACAACAATTCTAGGTCTTGATGA-TCAGAGAGCCAAGGAGATGCC
EST: gi|124933587|gb|EL010732.1|EL010732
EST:     ACCAAAAGGGGAGCACCTAAAGGCCATGAAG                         GTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCT
genomic: ACCAAAAGGGGAGCACCTAAAGGCCATGAAGgtactataaa ... ttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCT
EST: gi|125227780|gb|EL241865.1|EL241865
EST:     TATTGAATTTGCTGAAAAACCAAAAAGGGGAGCACCTAAAGGCCATGAAG                         GTTGACACAACAATTCTAGGTCTTGATGAT
genomic: TATTGAATTTGCTGAAAAACC-AAAAGGGGAGCACCTAAAGGCCATGAAGgtactataaa ... ttgctcctagGTTGACACAACAATTCTAGGTCTTGATGAT
EST: gi|125082756|gb|EL143555.1|EL143555
EST:     TTATTGAATTTGCTGAAAAACCAAAAGGGGAGCACCTAAAGGCCATGAAG                         GTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCA
genomic: TTATTGAATTTGCTGAAAAACCAAAAGGGGAGCACCTAAAGGCCATGAAGgtactataaa ... ttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcttcatcatgcggccttgtaaattaaaaaatctcgatttctttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG
                                        tttctttgctcct  CT-rich tract
                      taaattaaaaaatctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactataaactttacgctacttctctgcttcatcatgcggccttgtaaattaaaaaatctcgatttctttgctcctagGTTGACACAACAATTCTAGGTCTTGATGATCAGAGAGCCAAGGAGATGCCTTTCATTGCTAGTATGGGTATTTATGTTGTAAGCAGAGATGTAATGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG