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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacattcttgcccaaaatactcctcttggctacttgtatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G16830.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 15
gtatgacattcttgcccaaaatactcctcttggctacttg-tatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA
                        |  |||  | | | |  | | | |||  |||| |  |||      || || | ||   |  || |||||  | |||  |||  ||| || || ||||| ||||| || || || ||||||||||| ||||||||||  || ||||| || ||||| ||||||||| ||||||| |||||||
----------------------gttagtctatgttccctactgtgttaaacatttttttctctt----ttggtagtcta---aaactgtgtacattctat--cagGGTCTTCCACGGTTGAGGTTCAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGTGGACAATGGGTTTAAGATACTTGCAAATGCTGATGGACTCAGAA

upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 15
gtatgacattcttgcccaaaatactcctcttggctacttgtatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA
                           |  |  || ||  | |  |   |  |   | ||   |     || | | ||   ||  ||  |      |||  |||  ||| || || ||||| || || || || || ||||||||||| |||||||||||||| ||||| || ||||| ||||||||| ||||||| || ||||
-------------------------gttagtctctgctcattttcatgtttgtccttgtttctggaggggtcaatctaaccattttacat------tatgccagGCTCTTCCTCGCTTGAGGTTTAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGCAGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTTAGAA

upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 13
gtatgacattcttgcccaaaatactcctcttggctacttgtatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA
                           |  |  || ||    |  |   |  |   |  | | |     || | | ||   ||  ||  |      |||  |||  ||| || || ||||| ||||| || || || ||||||||||| ||||||||||  || ||||| || ||||| ||||||||| ||||||| |||||||
-------------------------gttagtatctgctcactttcatgtttgtccttgctttaggaggggtcaatctaaccattttacat------tatggcagGCTCTTCCTCGCTTGAGGTTCAATAAAGAAGGCAATCTTCTTGCTGTTACTACAGTGGACAATGGTTTTAAGATACTTGCAAATGCTGATGGACTCAGAA

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|47831151|gb|CK120835.1|CK120835
EST:     TGGACAATACAAATCTTTTGACAGTTGTTGAGGCTGAAGGTGGACTTCCG                         AATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACT
genomic: TGGACAATACAAATCTTTTGACAGTTGTTGAGGCTGAAGGTGGACTTCCGgtatgacatt ... tttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA
                           tactgat  putative branch site (score: 2)
                                             tttatttc  putative PPT
                                             tttatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacattcttgcccaaaatactcctcttggctacttgtatataaaatcttttgtattctcgagcctgttactttactgatgctatgtaccgtttatttcagAATCTACCCCGATTGAGATTCAACAAGGATGGGAATCTTCTTGCAGTTACTACAGCAGATAATGGATTCAAGATCCTTGCAAATACTGATGGTCTCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT