Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtattattgtgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaatacaatgttgttattagtcttaggttaggt...

Basic information

species Arabidopsis thaliana
transcript AT2G01250.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 5'ss of exon 3
TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgta-ttattgtgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaatacaatgttgttattagtcttaggttaggt
||||||||||||  |||| ||||| | ||||||| | ||||||||||||||||| |||||  ||||  || |     |  | |  ||     | ||||  ||||   ||| | | ||  ||   || |  | ||  |  | |||  |   ||       
TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtggttttcacaatcatttgaatgcacgtgttga--aattatgatatagtact--gtcaattgaggaaaaaatgttaatt--ttgcag-------

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 5'ss of exon 4
TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgt---tcgtgtattattgtgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaatacaatgttgttattagtcttaggttaggt-
|||||||||||| || ||||| || | ||||||||| |||||  ||||||||||||||||        ||  | |    ||    |   |  | | ||| | | |||  || || ||||  | |  |    |  |   |  | | |  |  || || |  | 
TATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactacttacaaatacaatttgagattcttttttgttggtcacttg--atgaattgct--gctagtgtttttgatcttaatcaatgcttgtaagtaacttg

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 5'ss of exon 3
TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcg-tgt---attattgtgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaat-acaatgttgttattagtcttaggttaggt
||||||||| ||  |||| ||||| |  |||||| | |||||||||||||||||||||||| | |||   |  ||||  | ||   |    |    | ||     |    ||  | | | | | | | |   | |||  |||    ||  ||| |  |     
TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAGgttagatgtcaaaccattgcatctggaaatgagaaatatatggctgttataaatctaataccatgctttgtgcttgacagcgttaagtttcttctcatat-----

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 5'ss of exon 4
TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcg-tgtattattg-tgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaatacaatgttgttattagtcttaggttaggt-------
||||||||| ||  || | ||||  |  |||||| | |||||||||||||||||||||||| | |||   |    ||  | || | || ||       || ||| | | |    |   |   |  | | || |  |||  ||   ||  ||| |||   |       
TATCAATGCTATGCACTCGAAGATGACAAAGATTTTGCAGCTCTTGCGTTTGAGACAGgttagatgtcaaaccactgcatctggaaatgaga-----aataaatggccgt----tataaatctaataccattctttgtgcttgacagcattaagtttcttctcatat

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|124919984|gb|EH993722.1|EH993722
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
EST: gi|164004646|gb|EL970618.1|EL970618
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTT-CCTT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTT
EST: gi|125010629|gb|EL082898.1|EL082898
EST:     AGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: AGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|124748702|gb|EH838832.1|EH838832
EST:     TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|125319309|gb|EL333394.1|EL333394
EST:     CTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGACT
genomic: CTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATG-CT
EST: gi|125049921|gb|EL122190.1|EL122190
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATAGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAAT-GGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
EST: gi|164037522|gb|ES122063.1|ES122063
EST:     GCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: GCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|164108779|gb|ES025314.1|ES025314
EST:     CGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|124812282|gb|EH897148.1|EH897148
EST:     TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|124984846|gb|EL057474.1|EL057474
EST:     ATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: ATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|164122478|gb|ES111041.1|ES111041
EST:     GCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: GCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|124799609|gb|EH889288.1|EH889288
EST:     GACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGA
genomic: GACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGA
EST: gi|164063060|gb|ES143257.1|ES143257
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGAT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGAT
EST: gi|124745629|gb|EH836441.1|EH836441
EST:     CTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|125242345|gb|EL256430.1|EL256430
EST:     TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGACTACGATGAACATGCT
genomic: TTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGG-CTACGATGAACATGCT
EST: gi|124983668|gb|EL056385.1|EL056385
EST:     AAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: AAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|163985597|gb|EL967501.1|EL967501
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTT-CCTT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTT
EST: gi|125191596|gb|EL206550.1|EL206550
EST:     CTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|164062187|gb|ES070866.1|ES070866
EST:     GCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTG-TTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: GCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|125221559|gb|EL235644.1|EL235644
EST:     CTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTAACGATGAAACATGC
genomic: CTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTA-CGATGAA-CATGC
EST: gi|164069432|gb|ES196094.1|ES196094
EST:     CATTGACCCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CATTGA-CCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|86082419|gb|DR378178.1|DR378178
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACAT-STT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|125100280|gb|EL155788.1|EL155788
EST:     ACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: ACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|164049079|gb|ES080861.1|ES080861
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCC
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCC
EST: gi|163968127|gb|ES170664.1|ES170664
EST:     GACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: GACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|164055456|gb|EL988624.1|EL988624
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAAC
EST: gi|125202366|gb|EL217320.1|EL217320
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|86082295|gb|DR378054.1|DR378054
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACAT-STT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|47828829|gb|CK118513.1|CK118513
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
EST: gi|124705769|gb|EH797171.1|EH797171
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAA
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAA
EST: gi|164081724|gb|ES106353.1|ES106353
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTT-CAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGAT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGAT
EST: gi|125276746|gb|EL290831.1|EL290831
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGA
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGA
EST: gi|125232096|gb|EL246181.1|EL246181
EST:     CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG                         ATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT
genomic: CCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtat ... tgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAGgttcgtgtattattgtgtttgtgtagattagtcttttgatgaattggcataaactgctaggttgtttcaatacaatgttgttattagtcttaggttaggt

- - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - -  CAGCTC