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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT

Basic information

species Arabidopsis thaliana
transcript AT4G32760.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcc--tctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
       ||| ||| | |        ||||  ||||   ||   ||  ||||     | | ||  |  || || |      || || | ||    | ||| ||||||||  |  |||| || || |||||||||||||| || ||||| || ||  | ||||||||||||||||||||||||| ||
gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcc--tctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
       ||| ||| | |        || |  ||||   ||   ||  ||||   | ||| ||   | || || |      || || | ||    | ||| ||||||||| |  |||| || || |||||||||||||| |  ||||| ||  |    ||||||||||||||||||||||||| ||
gttcaatatgcttcatgcttgcaaaactgtagttcttattctaatgaactgctggtttctgatggcattttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctcta---atcctaat-tggtctgatgca-----tatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
      |  | |||||  | |||  |     |||||     |  || | |     | ||   ||  | || |  | ||    |     | ||||| || || ||||||||||||||||| ||| | ||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| |  |
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
--------------gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtc-tgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
               | |   || || ||  ||  |   | ||||| | | | |         | | |     | ||| ||| ||     | ||||| || || ||||||||||| ||||| ||||| ||| | ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| | ||
gtatacataatttcttgaatatttttgcagctttctga-tgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtaatggttcttc-caaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtctgatgcat-atagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
                 |||    || ||       | || ||  ||  |  ||     |     ||| | | ||  || ||  ||||    ||   |||| || || ||||||| |||||||||  || | || || ||||| |||||||| || ||||| || || |||||||||||||||||||||||||| | ||
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgt-tcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|47828022|gb|CK117706.1|CK117706
EST:     TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAG                         CCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAA
genomic: TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAGgtaatggttc ... atgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAA
EST: gi|86063775|gb|DR359532.1|DR359532
EST:     TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAG                         CCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAA
genomic: TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAGgtaatggttc ... atgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAA
EST: gi|86063771|gb|DR359528.1|DR359528
EST:     TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAG                         CCGGACTTCSATGTCAAAGAGAAGATTCTGGTCCTTATCGATA
genomic: TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAGgtaatggttc ... atgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATA
EST: gi|86063777|gb|DR359534.1|DR359534
EST:     AGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAG                         CCGGACTTCCATGT
genomic: TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAGgtaatggttc ... atgcatatagCCGGACTTCCATGT
EST: gi|86063778|gb|DR359535.1|DR359535
EST:     TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGANGACG                         CCGGACTTCCATGTCAA-GAGAAGATTCTGGTCCTTATCGATACATGGCAA
genomic: TGGCTGAGAAAGGTGTTATTCATGAGATGGTCCGGATAGTTAAGAAGAAGgtaatggttc ... atgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctctctcccttgctctgcctctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
                                  taatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA