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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAAGAAGCATGGTTTGGAGATTTCTCAACCAGGCTTAGAGCCAAACAACGGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctttctctcactctctctctcttttacctttcctctgaattcgaatctgtctctaaggtttttgagtggttaacag

Basic information

species Arabidopsis thaliana
transcript AT1G08040.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 9
TTAAGAAGCATGGTTTGGAGATTTCTCAACCAGGCTTAGAGCCAAACAACGGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctttctctcactctctctct---cttttacctttcctctgaattcgaatctgtctc-----taaggtttttgagtggttaacag----------------------------------
| || ||  ||||||||||||| |||||||| ||  | ||||| || || ||| | |||||||| |||||||| ||||| ||||||  ||| || |||| |||     || | ||  || ||| |||   ||||   | ||  | | |    |  | | | |       | |  ||  ||   |||   |                                   
TGAAAAAATATGGTTTGGAGATCTCTCAACCTGGTCTTGAGCCTAATAATGGATTGACATGGGAGATGACAAAAAGGAGGGGTGACAAAGAAGTTCACATgtattcctttgcccttcctttctttcttaactttagtcattgatgtaataaggtgttttttttcgtatcatgacttcagatgtgttcttaagtcttgacacatttttgtgtgtgttggcaaatag

upper sequence: AT1G08040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 9
TTAAGAAGCATGGTTTGGAGATTTCTCAACCAGGCTTAGAGCCAAACAACGGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctttctctcactctctctctcttttacctttcctctgaattcgaatct-gtctctaaggtttttgagtggttaacag---------------------------------------------------------------------
| ||||| || ||||||||||| |||||||| ||  | ||||| || || ||| | |||||| | ||||||||||||||||||||| |||| || |||||||| |   | |  ||| ||||| | |||| |  || |  |||    |      || || ||| |  | |   |||  | ||                                                                        
TAAAGAAACACGGTTTGGAGATCTCTCAACCTGGTCTGGAGCCCAATAATGGATTAACATGGCAGATGACAAAGAGGAGAGGTGACAGAGAAGTTCACAAgtaggctttgttgctctctctccccctctctccccctctctccccctcttcccctagtatcttatttctgcaagttctaaattctgtattgtgccccttccctaatatcttatttttgcaagttctaaattctgtattgctgattggtgacag
















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|86085178|gb|DR380937.1|DR380937
EST:     GACTTACATGGGAAATGACAAAAGAGGAGAGGTGACCGAGATGTCCACAA                         AGAAACTAAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATG
genomic: GACTTACATGGGAAATGAC-AAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctt ... tggttaacagAGAAACTAAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATG
EST: gi|124764467|gb|EH854597.1|EH854597
EST:     AATGACAAAGAGGAGAGGTGACCGAGATGTCCACAA                         AGAAACTAAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATG
genomic: AATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctt ... tggttaacagAGAAACTAAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATG
EST: gi|164010653|gb|ES169529.1|ES169529
EST:     GGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAA                         AGAAACTAAGGAAAAACCAGGATGGTGCAGTGAT
genomic: GGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctt ... tggttaacagAGAAACTAAGGAAAAACCAGGATGGTGCAGTGAT
EST: gi|125189380|gb|EL204334.1|EL204334
EST:     GGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAA                         AGAAACTAAGGAAAAA
genomic: GGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctt ... tggttaacagAGAAACTAAGGAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAAGAAGCATGGTTTGGAGATTTCTCAACCAGGCTTAGAGCCAAACAACGGACTTACATGGGAAATGACAAAGAGGAGAGGTGACCGAGATGTCCACAAgtaagagctttctctcactctctctctcttttacctttcctctgaattcgaatctgtctctaaggtttttgagtggttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG