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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA

Basic information

species Arabidopsis thaliana
transcript AT4G39960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 4
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgct--tttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                                     |  |  | | |   | | |||| |  |     |    | | | ||| ||| | || |  | ||  | ||   | |||| | ||      |   |||||| |||| ||||||||||| |||||||| |||||||||||||| |||||
-----------------------------------------------------tccaataat-acagtgcacttttaaaaataaaaccaatgctgattt-aagatatgatgatatcacttgtaacaaaatggtcctgaatc-cttttattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA

upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 4
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                              | |  |   |   | |||      |     ||||  || || |    | | |  | |||||  | || |||  | ||    || | ||      |   |||||| |||| ||||||||||| |||||||| |||||||||||||| |||||
---------------------------------------------tagtagtacctgatactgaatagagt-----atgaatttgatatacataacatg-atgttgtattgtt-tattttctg-tgttggtcctgaatc-cttttattttccagCCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA

upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 4
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgat-tctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                                || ||  ||  ||| |  |   | |   |     || ||||||| |   | | |    ||  |   |||| | | | | |  | |||||| || ||  ||||  |||||||||||||||| ||  ||||||||||||| |||||||||||
----------------------------------------------gttcctgcatatgatttacttgagtgtgc-acatcttttatgtgttgattgtctga----tgtatcattataatatcaaatttctctctactttggac--attt--cagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA

upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G38040.1 (Glycine max), 3'ss of exon 4
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacct---attttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                                     |   |||   ||| ||  |||   || |||   |   ||  |  | ||| |||| || || |||  ||  |  || |   | ||||  || |   |  || |||||||||||||||| ||  |||||| |||||| |||||||||||
-----------------------------------------------------tcctgcaaatatgatttacttgagtgtgctcttt---ttttgtgtgtaaattgt-ctgttatatccttacaatataaaatttctctctactttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTGTCATCCTGATGTGAACAA

upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                               || ||||||  ||    ||    |     ||    ||    |   | |||||  |    |||  |  ||||   | ||  ||  | |||||| ||    | ||| ||||||||| ||||| || ||||||||||||||||||||||||||
-----------------------------------------------cttatgtgttacaa-actgaagttgaagaattgtttttgcatagcctgctttatatccttgcactaatataaccttactctg--tgtactcttca----tcttgtagCTTATCGAAAGCTTGCCAGGAGTTATCATCCAGATGTGAACAA

upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                                                                                  ||    |   | |||||  |    |||  |  ||||   | ||  ||  | |||||| ||    | ||| ||||||||| ||||| || ||||||||||||||||||||||||||
-------------------------------------------------------------------------------gtttttgcatagcctgctttatatccttgcactaatataaccttactctg--tgtactcttca----tcttgtagCTTATCGAAAGCTTGCCAGGAGTTATCATCCAGATGTGAACAA

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|125187553|gb|EL202507.1|EL202507
EST:     TTCTGTCCTTGGAGTCTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCG                         CTTATCGGAAGCTCGCTA
genomic: TTCTGTCCTTGGAGTCTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCGgtatgcaatt ... tattttgcagCTTATCGGAAGCTCGCTA
EST: gi|124977810|gb|EL051088.1|EL051088
EST:     CTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCG                         CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
genomic: CTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCGgtatgcaatt ... tattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
EST: gi|86057935|gb|DR353692.1|DR353692
EST:     TTCTGTCCTTGGAGTCTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCG                         CTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAGGATGCTG
genomic: TTCTGTCCTTGGAGTCTCGAAAAATGCAACCAAAGCTGAGATTAAAAGCGgtatgcaatt ... tattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAAGGATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
                   gtttgac  putative branch site (score: 4)
                                           cctatttt  putative PPT
          ttttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgattctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG