Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctactttcatccatcttctactttaatcttgtttcaatataattttgtgtgaaccatgtatcttctcttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTTGATTACAGGCTCGCTGCTCTTCCCCCTAGTGCCAAGGGTCTTGTTGTAT

Basic information

species Arabidopsis thaliana
transcript AT5G58260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G31620.1 (Glycine max), 3'ss of exon 1
-----------------gtatgtctactttcatccatc-ttctactttaatcttgtttcaatataattttgtgtgaaccatgtatcttctctt--cttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTTGATTACAGGCTCGCTGCTCTTCCCCCTAGTGCCAAGGGTCTTGTTGTAT
                 || | |  || ||  |   |  ||||   |  || || | ||| |  || || || |  || | | || || || |   ||| || ||||| ||||||| || || |||||||| |||||||  ||||||||||||||||||||  | |  ||  | || || | |||||| || || || || |
accaccatctaagttttgtcttttaacattttttggttgttcttgatggatgttatgtcact-caagttagtttacactaag-attttgtcatgaatttcagCCTCATGTTGGGAAGCAGCCAATAGCAAGGTGGTATTTCCCACCAGAAGTTGATTACAGATTAGAAGCATTGCCACCAAATGCCAAAGGACTGGTGGTGT

upper sequence: AT5G58260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G05640.1 (Glycine max), 3'ss of exon 1
-----------------gtatgtc-tactttcatccatcttctactttaatcttgtttcaatataattttgtgtgaaccatgtatct-tctcttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTTGATTACAGGCTCGCTGCTCTTCCCCCTAGTGCCAAGGGTCTTGTTGTAT
                 || | |  || |||  |   | ||||   |  || || | ||| |  | |||  | |  || |   || | ||     ||| || ||||| |||| || || || |||||||| |||||||  ||||||||||||||||||||  | |  ||  | || || | |||||| ||  | || || |
atcaccatctaagttttgtctttaatatttttttggttattcttgatggatgttatgtcactcaagtttaat-tacactaaaaatttgtcatgaatttcagCCTCATGTTGGCAAGCAGCCAATAGCAAGGTGGTATTTCCCACCAGAAGTTGATTACAGATTAGAAGCGTTGCCACCAAATGCCAAAGGATTGGTAGTGT
















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|124716473|gb|EH807875.1|EH807875
EST:     TCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGTTATTATCCACCAGA
genomic: TCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGA
EST: gi|86018485|gb|DR314231.1|DR314231
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
EST: gi|86018480|gb|DR314226.1|DR314226
EST:     CCTTGGTAGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCA
genomic: CCTTGGT-GACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCA
EST: gi|86018483|gb|DR314229.1|DR314229
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
EST: gi|86074812|gb|DR370569.1|DR370569
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
EST: gi|86018481|gb|DR314227.1|DR314227
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGNTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
EST: gi|86018484|gb|DR314230.1|DR314230
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTT
EST: gi|116477443|gb|EG520035.1|EG520035
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GCTCATCTTGGGAAAC
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagGCTCATCTTGGGAAAC
EST: gi|124979959|gb|EL052952.1|EL052952
EST:     GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCT                         GACTCATCTTGGGAAACAACCTATAGCAAG
genomic: GCCTTGGTGACCCTGAGACTACCCTTCTCAAGAACTACCCTGTTTGCCCTgtatgtctac ... cttcttttagG-CTCATCTTGGGAAACAACCTATAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatcttgtttcaatataattttgtgtgaaccatgtatcttctcttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTTGATTACAGGCTCGCTGCTCTTCCCCCTAGTGCCAAGGGTCTTGTTGTAT
 ctttaat  putative branch site (score: 4)
                                ccatgtatcttctctt  putative PPT
       ttgtttcaatataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctactttcatccatcttctactttaatcttgtttcaatataattttgtgtgaaccatgtatcttctcttcttttagGCTCATCTTGGGAAACAACCTATAGCAAGATGGTATTATCCACCAGAAGTTGATTACAGGCTCGCTGCTCTTCCCCCTAGTGCCAAGGGTCTTGTTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT