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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatctatccttaatcttttctgttaggttctataactgtttcattgcaaggaattggcaaattgaaaaccatgggatcttcttgaattatatctaatctcataatattcttcatgctgcag

Basic information

species Arabidopsis thaliana
transcript AT4G23100.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 10
GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatctatccttaatcttttctgttaggttctataactgtttcattgcaaggaattggcaaattgaaaaccatgggatcttcttgaattatatctaatctcataatattcttcatgctgcag
||||||||  ||||| ||||| ||| | |||||||| ||||| |||| |||  |||| || || ||||| ||||||||||||||| |||||||||||     || |   |  |   ||       ||||| | |    |     | |  |  ||||| |  |  ||  ||     |  |  | || || |   | |    | |||||  |  ||| |   
GTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTATCGAAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGGgtctcttcctgtttgtgttaccttagtgcttgttctgtta----tatgcagtagagctttggcta--tagaatacagaacttggttattaactagactaacttgatttatatttgttttgcag---

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 10
GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatctatccttaatcttttctgttaggttctataactgtttcatt--gcaaggaattggcaaattgaaaaccatgggatcttcttgaattatatctaatctcataatattcttcatgctgcag
 |||||||  ||||| ||||||||| | ||| |||| ||||| |||| |||  | || || || ||||| ||||||||||||||| |||||||||||    ||| ||||   ||| ||   ||||    | |  |||||  ||   | |  |  ||||| |  |  ||  ||     |  |  | || || |   | |    | |||||  |  ||| |   
ATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGGgtc----tct-tcctgtttctgttaccttagtgcttgtg-ctgttatatgcagtagagctttggcta--tagaatacagaacttggttattaactagactaactggatttatatttgttttgcag---

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 10
GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatctatccttaatcttttc----tgttaggtt--ctataactgtttcattgcaaggaattggcaaattgaa-------aaccatgggatct------tcttgaattat---atcta---atctcataatattcttcatgctgcag
|||| ||||||||||||| || ||||| ||||| |||||||| |||| |||  | ||  ||| ||| |||||||||||||||| ||| ||  ||||    ||||||| ||||| || |     | | ||| |  ||||    |   |          ||||  ||| | |         ||||| | ||        |||||| || |   || ||   |  | || || || ||  |  |||||
GTTTCAGCAGTATGTTGATTATGCACTTGATGTTCCTATGTATTTTGTCTATCGGAAACACAGATATATCGACTGTACTGGAAAGACCTTCAGGgttcccatctatctttaatattcttgtaatttaaggctatctattgtagccccgacattctttattgtgaaacttactttgcttgaccatagtatacacgtagtcttgatttgttcaatgtagagaattgattatttttttt-tattgcag

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|125225904|gb|EL239989.1|EL239989
EST:     TACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG                         CAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT
genomic: TACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatct ... catgctgcagCAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT
EST: gi|125222965|gb|EL237050.1|EL237050
EST:     TTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG                         CAATTCTTGGCTGGAAAACTTCCCTGT
genomic: TTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatct ... catgctgcagCAATTCTTGGCTGGAAAACTTCCCTGT
EST: gi|47830326|gb|CK120010.1|CK120010
EST:     TTGCCTACAGAAAGAACAAATACATCGACTGTACTGNAATGACATTTCGG                         CAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGNTGA-CTGCCTTCATA
genomic: TTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatct ... catgctgcagCAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGG-TGAACTGCCTTCATA
EST: gi|124797477|gb|EH887156.1|EH887156
EST:     AATACATCGACTGTACTGGAATGACATTTCGG                         CAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT
genomic: AATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatct ... catgctgcagCAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT
EST: gi|125318037|gb|EL332122.1|EL332122
EST:     TTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG                         CAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT
genomic: TTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatct ... catgctgcagCAATTCTTGGCTGGAAAACTTCCCTGTCTCCCTGGTGAACTGCCTTCATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGGgtcaaaatctatccttaatcttttctgttaggttctataactgtttcattgcaaggaattggcaaattgaaaaccatgggatcttcttgaattatatctaatctcataatattcttcatgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC