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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgggatattgctcctttgatttcgtcctttctgctct...

Basic information

species Arabidopsis thaliana
transcript AT4G24770.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G011129_T01 (Zea mays), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgg--gatattgctcctttgatttcgtccttt-ctgctct--
 || ||||| || ||||| || || |||||||||||||| ||||| || |||||  |||| || || |||||||  |||||||||| |||| | || ||||| ||||||| || |    ||| |||   |||  | ||| |||   |||     |||| || ||||   |||| ||   |||| ||  | | ||| |  |||   
CATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCTATgtgagtttat-tgat---gactatcagctattaatttttttgacagattt-tgggtatagttatggttaatatggcctgtttgcttatgccatttgcaactcatt

upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G123234_T02 (Zea mays), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgggatattgctcctttgatttcgtcctttctgctct---
||| ||||| || ||||||| |||||| ||||||||||| ||||| || |||||  |||| || |||||||| | |||  | |||| ||||| ||| |||||||| | || |   ||     ||   ||  |||| || | ||| ||| | || | ||||| ||    ||   |||  | | |||| ||  |  | ||     
TATCTACAACAGAGAAACTGGCCAGAGCCGTGGGTTTGGTTTTGTTACCATGAGCACTGTTGAGGAAGCTGACAAAGCCATTGAGATGTTCAGCCGCTATgtaagctcatttatgtcctctcttttctctgttcttttccagagctatga-ca-gaattgtaatccactaaatctcaat-gctttcctctgtattccttcatg

upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G18470.1 (Glycine max), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgggatattgctcctttgatttcgtcctttctgctct----
||| || || |||||||||||||||||||| |||||||| |||||||| |||||| |||| || |||||||| |  ||||||||||| |||||||| |||||||||| ||||      |||||    |  ||||   |    | ||    | | |  |||  |       ||     || |  ||     | | ||   |    
TATTTATAACAGGGAAACTGACCAGAGTCGCGGGTTTGGGTTTGTGACGATGAGTACTGTTGAAGAAGCTGAAAGCGCTGTGGAGAAATTCAACCGCTATgtaagttgatatat----aacttgttttgttttcaaatgtgaatttggggggaggggttgaaaaattcggtttgattttcgtattgaatttatgtgtggttatg

upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G36420.2 (Glycine max), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagtta--ttagcat-gtattgtgatgggatattgctcctttgatt-tcgtcctttctgctct
||| || ||||||||||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||||  || |||||||| ||||  ||||| ||||||||||     ||||   ||   |  | |   |||  ||||||  || | || | | | ||  | || |       ||||||  ||||  | | |     
TATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttattgatatcaattgttttgtactctaattttacgagttagcttgggattgaaatttggggtgaaaagttcggtttgatcatcgtattgtgtt----

upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G02800.1 (Glycine max), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaact--ttcaatcatttctgtttctgagttattagcatgtattgtgatggg-atattgctcctttgatttcgtcctttctgctct
||| || |||||||  ||||||| ||||||||||||||||||||| || |||||| |  | || ||   | |||  ||||| |||| |||||   |||| |||||||  | | |||     |  ||||   ||||    || || |   |  |   | || ||  | |  ||  |      || |  | |     | ||    
TATTTATAATAGGGCCACTGACCGGAGTCGTGGGTTTGGATTTGTTACCATGAGTACACTTGAAGAGCTTAAGAAGGCTGTCGAGATGTTCAGTGGTTACgtaagttgttgttgttgttgttagttcatatattttgtattgtgtgacttcggtgagaatggtcctcgttatggtctaatgttcaagtggaaaactgtgt---

upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0066g00140.t01 (Vitis vinifera), 5'ss of exon 2
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttca-atcatttc--tgtttctgagttattagcatgtattgtgatgggatattgctcctttgatttcgtcctttctgctct
 || |||||||| ||||| || ||||||||||||||||| ||| | ||||||||  |||| || || || || |  |||||||||| ||||||||| ||||||||||  |    ||| | |  |||  | | ||   |||||    |||    |   ||   ||| ||||  | ||   |   || |  |    |  | || |
AATTTACAATAGAGAAACAGATCAGAGTCGTGGGTTTGGGTTTATAACAATGAGCACTGTTGAAGAGGCCGAAAAGGCTGTGGAGATGTTCAACCGATATgtaagttgcttgttttctatcaatcatgttactttgttgttttctggtttcctgtgggtgg-gtggtggggaagtgaaacaaagaat--gaagatgatacttt

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|124779946|gb|EH869889.1|EH869889
EST:     TTCTGTGGACGAAGCTGAGACGGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACG
genomic: TTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACG
EST: gi|125323699|gb|EL337781.1|EL337781
EST:     ACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
genomic: ACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
EST: gi|125315266|gb|EL329351.1|EL329351
EST:     CTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
genomic: CTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
EST: gi|124944213|gb|EL020334.1|EL020334
EST:     GAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAAGAGGATC
genomic: GAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAA-GAGGATC
EST: gi|86087405|gb|DR383164.1|DR383164
EST:     TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
genomic: TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
EST: gi|124892474|gb|EH971376.1|EH971376
EST:     TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAA
genomic: TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAA
EST: gi|124710564|gb|EH801966.1|EH801966
EST:     TGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
genomic: TGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGCTCCAAGAGGATCA
EST: gi|124993949|gb|EL066218.1|EL066218
EST:     TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGC
genomic: TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAGC
EST: gi|124709260|gb|EH800662.1|EH800662
EST:     TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGGCAG
genomic: TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGGCAG
EST: gi|125001393|gb|EL073662.1|EL073662
EST:     TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTAT                         GATCTTAACGGACGTCTACTAACTGTAAACAAGG
genomic: TGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttat ... tgtgtttcagGATCTTAACGGACGTCTACTAACTGTAAACAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagttattagcatgtattgtgatgggatattgctcctttgatttcgtcctttctgctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT