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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattagaagacatttatatttactggtcttttgctcattggatgaaattcaccagaattttttgatgtctttttctctcaaatacgttgatttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG

Basic information

species Arabidopsis thaliana
transcript AT1G09100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------gattagaagacatttatatttactggtcttttgctcattggatgaaattcaccagaattttttgatgtcttt----ttctctcaaatacgttgatttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG
                                                            |    | || ||   |   | |||   |   |  |||||| |   |  || |  |  | ||||   |||    || | |    |  | |  |     | |||| ||   |||| |||| ||| | ||  |||||||  | |||||||| || |||||||||||||||||||||||||| ||||| |||||||| ||| | |
gcaagcccgcctccgctctctctctctctcccctaaccctagatccccctccctccgaggtttttgccagttgcctcctccggtgaatctttgcttggattagggtttccggg-tcgtctgatcggtttggggttttttttggtgtgattttggtgcgcagGATGAGCTGCAGCGGACCAACTTGGAGCTGGAATCGTTCAAGGAGAAGATTAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTTCCCTACCTCG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 1
gattagaagacatttatatttactggtcttttgctcattggatgaaattcacca--gaattttttgatgtctttttctctcaaatacgttgatttgttgta------------gGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG
| ||        | | | | | |   ||    |   |    |     | | |||  ||  |  |  |||   |||  ||| |  |  |  | |||||   |            ||| ||   |||| |||| ||||||||  |||||||    |||||||| || |||||||||||||||||||| || || ||||| ||||| |||||| | |
gtttgctctctctctctctctccgcctccgcgggaaaccctagcttttgccccagcgatctcctccatgggatttggtctgatttgtgggggtttgtctcatcgggtgcctcagGATGAGCTGCAGCGGACGAACCTTGAGGTGGAATCCTACAAGGAGAAGATCAAGGAGAACCAGGAGAAGATCAAACTCAACAAGCAGCTGCCTTACCTTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 1
gattagaagacatttatatttactggtcttttgctcattggatgaaattcaccagaattttttgatgtctttttctctcaaatacgttgatttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG
  |  | | ||  |     |  |    |   ||| | | |     | |   |  || | || |||| |  |||    |    |  | ||  |  |  ||||| ||   |||| || | ||||| ||  |||| ||  | |||||||| |  |||||||||||||||||||||||||| ||||| ||||| || ||| | |
-gtgcggaaaccctagccctagcc---ccgctgcgcgtcgcccagagtgt-cgggactgttctgat-tgatttgggatgttttgggctgggtgttcatagGACGAGCTGCAGCGGTCGAACCTGGAGCTGGAGTCTATCAAGGAGAAGACCAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTGCCGTACCTCG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 1
gattagaagacatttatatttactggtcttttgctcat-tggatgaaattcaccagaattttttgatgtctttttctctcaaatacgttgatt--tgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG
            | |||  |  ||  | || |  | || |   ||   |||      ||  ||||   | ||  |   |       || |  |  ||||| |||| || | ||||||||| ||| | || | ||| ||    |||||||| || |||||||| ||||||||||| ||||| ||||| |||||||| ||||| |
---------gtctctattctctctctttttctctttatatatgtgtctttccgtgatatgatttgcgattttgatgaatggtggtggtggtatggtgttgaagGAGGAGTTGCAGAGGACGAACATGGAGTGGGACTCCTATAAGGAGAAGATCAAGGAGAATCAGGAGAAGATCAAGCTCAACAAGCAGCTTCCCTACTTGG

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|86061011|gb|DR356768.1|DR356768
EST:     ACATCGGTAGAGCTTCTCNTCTCTTAGCCAACGAGATTCGCATCCTCAAG                         GAAGAATCGCAGA
genomic: ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAGgtcaccaccc ... tttgttgtagGAAGAATCGCAGA
EST: gi|86061010|gb|DR356767.1|DR356767
EST:     ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAG                         GAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA
genomic: ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAGgtcaccaccc ... tttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA
EST: gi|124892867|gb|EH971769.1|EH971769
EST:     ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAG                         GAAGAATCGCAGAGGACAAACCTTGATT
genomic: ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAGgtcaccaccc ... tttgttgtagGAAGAATCGCAGAGGACAAACCTTGATT
EST: gi|164109943|gb|EL974534.1|EL974534
EST:     AGAGCTTCTCGTCTCTTAGCCAACGAGTATTCGCATCCTCAAG                         GAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA
genomic: AGAGCTTCTCGTCTCTTAGCCAACGAG-ATTCGCATCCTCAAGgtcaccaccc ... tttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA
EST: gi|86061012|gb|DR356769.1|DR356769
EST:     ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAG                         GAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA
genomic: ACATCGGTAGAGCTTCTCGTCTCTTAGCCAACGAGATTCGCATCCTCAAGgtcaccaccc ... tttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcaccagaattttttgatgtctttttctctcaaatacgttgatttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG
          aattttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattagaagacatttatatttactggtcttttgctcattggatgaaattcaccagaattttttgatgtctttttctctcaaatacgttgatttgttgtagGAAGAATCGCAGAGGACAAACCTTGATTTGGAATCAGTGAAGGAGAAAATAAAGGAGAACCAGGAGAAGATTAAGCTTAACAAACAGCTTCCTTACTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - -gaagaca
- - - - - - - - - - - - - - - - - - - - gatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - -caccaga