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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA

Basic information

species Arabidopsis thaliana
transcript AT1G77590.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
          | |  |  |    ||   |||| ||    | |    |||| ||| || |      | |  |   |   || ||   |  | | || ||| || |||||  | | || |||||||| || |||||||| || || ||||| |||||||| ||||||||||| |||   || ||||   
-------gtgactctaaaatagcatctatttacatcatcggtt---acttaagattaataactcactgtatggatttttttttcagGCAC-TCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT

upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 4
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
||  ||  |   |      |||  |       ||  |    | || || | |    |   | |    |    || | |  | | |   ||  | |   || |    |  || | |     | | |  |    | |    | | |||   |||||  |                              
gttcctataggatatggatctcctttgacccttactgatacttcaaacatgattaaaaagggacaaagGGGGATGCTACAGCTCTGAGGCCAACT--TTAATGGCAGCTGTACCAGCAATTCTTGACCGTGTTCG----TGATGGAGTGTTCAAGAAG-----------------------------

upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
----------------------------------------gtatcttaaaagttcattactcaatgcgtttatatagcagttccacac-ttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
                                          |  ||||| |    |||     ||  ||  | |   | ||   |   |   |  | |||  |      | ||| |  ||||| ||||   | || ||  || ||||  ||  ||| |||||||| ||||| |||||  |||| ||||| |||||||| ||||||||||| | | | || |||  ||
gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatttttcttatgttggatgttttgacaaactcaaatac--ttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA

upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ35799 (Selaginella moellendorffii), 3'ss of exon 4
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
                        |  | |  | | |   |  | |   || ||  |   ||    |    |  |  |  || | |||     |||  | ||   ||   ||| |||||||||||||| || ||||| || |||||||| || | ||||||||||||||| || ||||| || ||  
-----------------------gtaagctc-tgtggttttctctcgtctcggaagaaaagacactgatacatgtttagcgt-gcagACTACTATGTGTGCTGCCGGTGTTGCCATTGGATATGGGTCGCCATTGACCCTGACGGATACGTCTAGCAAGATAAAAAAGGGGACCAAAGGTGACGTTG

upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ36404 (Selaginella moellendorffii), 3'ss of exon 4
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
                        |  | |  | | |   |  | |   || ||  |   ||    |    |  |     || | |||     |||  | ||   ||   ||| |||||||| ||||| || ||||| || |||||||| || | ||||||||||||||| || ||||| |||||  
-----------------------gtaagctc-tctggttttctctcgtctcggaagaaaagacactgatacatatttggcgt-gcagACTACTATGTGTGCTGCCGGTGTTGCCATTGGATACGGGTCGCCATTGACCCTGACGGATACATCTAGCAAGATAAAAAAGGGGACCAAAGGTGATGTTG

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|19875635|gb|AU236466.1|AU236466
EST:     TTTACCTTTGGCTCACATCCTTGAGTTAGCAGCTGAG                         AGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACG
genomic: TTTACCTTTGGCTCACATCCTTGAGTTAGCAGCTGAGgtatcttaaa ... attgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA
                                   gcctaat  putative branch site (score: 3)
                                         ttccatt  CT-rich tract
                       tatttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG