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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtccaaatgtgttaatgatctgttgattttttaatcag

Basic information

species Arabidopsis thaliana
transcript AT4G13170.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtccaaatgtgttaatgatctgtt--gattttttaatcag----
| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  |||||||||||| ||||||||||||| |||||||   | || |  | |||| ||||| |    |   | ||| |   ||||||    |     |    ||   | || ||   | |  || ||       
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaagactttttctactgtttttttatgctaatatatttaattttaatatagtttg-ataggcctacactagcaacctatttgaaatcattcattgtacat

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgtta--tgttttgtttcatgattctgtaatagttaatgtccaaat-gtgttaatgatctgttgattttttaatcag----------------------------
| |||||||| |  || || || ||||| |||||||||| ||||||||| || ||||| || |||||||| |||||||||||| |||| |||||||| ||||||||  |||||| | ||||  | |  ||||||   |  | ||  | ||||  ||||| |  ||||  | | | |  | | ||  | || | |  |                             
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatt-taatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G02790.1 (Glycine max), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgttt-catgattctgtaatagtt-aatgtccaaatgt--gttaatgatctgttgattttttaatcag-
| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  |||||||||||| |||||||||| || |||||||   | || ||| ||| ||    |||| |||| ||  ||     || |||| |||   ||  | |  |  |   ||| |      | || || |  
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCACTCAAgtaagagtttttctgtctttctgaatcgtttagttttcaatatgtgtcaagagtttaataagcacgtattagcgacaaatcagaaatgatgttgataaat

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G46860.1 (Glycine max), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtccaaatgtgttaatgatctgttgattttttaatcag
| ||||| || |  ||||| ||||| || |||||||| | |||||| || || |||||||| |||||||  ||||| |||||| ||||||||||||| |||| |||| |  ||| |  ||||||| ||     |||  |  |||  |  |  |  |||   || || || |||||       |||| |||     
CAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagtttttctttctacttttgttttgga--atttggttgttcaatcttt-tagatgctgaagtg-gtgaatga------aatttattag----

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaat---agttaatgtccaaatgtgttaatgatctgttgattt--tttaatcag-------------------------------------------
|||||||||| || || || ||||| || ||||||| || |||||||||||| || || || || ||||| ||||| ||||| ||||||||||| || |||| |||| |||| | | | ||  ||||   |||| ||   |||   ||||    |||    | ||| | | ||  |  | |  | || |  |||||||                                             
CCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtt-tcttgtttctcttgattat-cgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattag

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 5'ss of exon 2
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctct-tttg---tttttttgttatgttttgtttcatgattctg--taatagttaatgtccaaatgtgttaatgatctgttgatttttt-----aatcag
| |||||||| || || || |||||  | ||||||| ||  ||||| || |||||||| || || ||||| ||||| |||||||||||||| ||||| |||| |||||| | ||||   ||| ||| |||| |||| |||  |  ||  |  ||  | ||  |||     || |    | ||   |    |||||     ||||||
CTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTTATTCCTGACGCTCTCAAgtgagttctgtatttgagttttattttttattttttattttttatttaggcctataaattcttgttggtttgagactttaatgcttgagatttttgggaaaatcag

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S165_40V6.1 (Physcomitrella patens), 5'ss of exon 3
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatg--attct---gtaatagttaatgtccaaatgtgttaatgatct--gttgattttttaatcag
||||| | ||||||||||| ||||  ||||||||||  ||||| ||| ||||  | || || |||||||| || ||||||||||| || |||||||| |||| |||| ||  |   | | |    ||| |    || |||  |||||    |||||   ||  | || || |      | | |  | ||  ||   |||   
CCAAGAGGGGTGCTGCTGCTCTTGAGCGCTTGAAGGCCTTTGAAGGAGTCCCTGCACCGTATGACAAGATGAAAAGAATGGTTATCCCCGATGCTCTCAAgtgagttatcaatctctctctaaaaatgatgcaatttatgctattcttggataatatgaaaaatgcagatatcacgcgggttttagctgcattggcaatg--

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S174_48V6.1 (Physcomitrella patens), 5'ss of exon 3
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtc-caaatgtg--ttaatgatc--tgttgattttttaatcag--------------------------------------------------------------
| ||| | || |||||||| ||||  ||||||||||  || |||||  ||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||| | |  ||||       | |   ||| |  | ||| ||     | ||| || | ||  | | | ||  |  | || |  ||| |  | ||    |||                                                              
CAAAGAGGGGAGCTGCTGCTCTTGAGCGCTTGAAGGCATTCGAGGGTGTCCCAGCTCCTTACGACAAAATGAAGAGGATGGTCATTCCTGATGCTCTCAAgtatgctaactttc------tcgcactgtctgatgtcaagaagtgattataatttaggttaccagtatgattcgaggaccaatgtaggctgttgctgcagaattgttttagactaataaatcaatgttattgtgtcgttcatgagacgttttatttatgcag

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|116477676|gb|EG520268.1|EG520268
EST:     CCCCCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
EST: gi|116477675|gb|EG520267.1|EG520267
EST:     CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
EST: gi|124994651|gb|EL066920.1|EL066920
EST:     ACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
genomic: ACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
EST: gi|125187939|gb|EL202893.1|EL202893
EST:     CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCA
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCA
EST: gi|164028227|gb|ES193540.1|ES193540
EST:     CGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTAATTGGGACGTCTAT
genomic: CGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTA-TTGGGACGTTTAT
EST: gi|125294108|gb|EL308193.1|EL308193
EST:     CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
EST: gi|125319756|gb|EL333841.1|EL333841
EST:     CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTAT
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTAT
EST: gi|164039770|gb|EL995438.1|EL995438
EST:     TTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTCTATC
genomic: TTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTATC
EST: gi|124945018|gb|EL021065.1|EL021065
EST:     CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAA                         GGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTA
genomic: CCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctc ... ttttaatcagGGTTTTGAGACTTCAGAGTGGTCACAAGTACTGCTTATTGGGACGTTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgttatgttttgtttcatgattctgtaatagttaatgtccaaatgtgttaatgatctgttgattttttaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA