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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcatccactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA

Basic information

species Arabidopsis thaliana
transcript AT3G48750.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcat--ccactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
                                                                        |  |||| |  ||     ||| ||||| ||    | ||||| |    |  ||  | || |   |         ||||| | |  |  || | | ||| | |  || |||||||||||||| || |||||||| |||||||| ||  | |||||||| || ||| ||||||| |||||  || |||| ||||| || |
gtaagatgttgaaactaacatcctcttttcattgatgcaagtatcacgccatttagtgatagtaacttcgctgaaagtg-tgggatgagctagccattgcttccattttgtgcatggttt--atgttgaa-acgggaaatgtgatgctgtcctttgcgcctgtgtgcagTCGTTCCTCTACCAGATTCTCCGGGGCATTGCGTACTGCCACTCGCACCGTGTTCTCCACCGAGATTTGAAGCCCCAGAACCTGCTGATAGATCGGCGTA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 3
-gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagct---gatcagagctgttcatcca--ctattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
  |   |  | |     | ||         |  ||  | || | ||| | |  | | | | |    |    ||  ||  |  | |   |  || | | ||||  |  ||||| || |||||| |||| ||||| || || || || ||||| ||||| ||||| ||  |||| ||||||||||||||||| |||||||| |
tctattttgtcaagggttatataagggagatgctaattttggtgaaaat-accagttagtttggatttaaaatttgaattccttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
----gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcatc-cactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
     |  ||  |  |  |  ||||| |     | || |  |||   | ||    || |    ||       |   |    || ||    || | | ||||  |  ||||| || |||||| |||| ||||| || || || || ||||| ||||| ||||| ||  |||| ||||||||||||||||| |||||||| |
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataa--gctgatcagagctgttcatccacta----ttttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
 |   || |    |  |||     |  ||| |||| | |   |   |  |    |  | ||||  |       | |||  | |  |   |    ||| ||||  |  ||  | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| ||| ||||||| ||||| ||  | || ||||| || |
-tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcgatggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA

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|301501515|gb|HO207055.1|HO207055
EST:     AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAA                         ACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGG
genomic: AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAAgtgagtgcta ... ctattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGG
EST: gi|164074130|gb|ES039780.1|ES039780
EST:     AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAA                         ACATATCTTTACCAGATTCTCCGTGGAAT
genomic: AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAAgtgagtgcta ... ctattttcagACATATCTTTACCAGATTCTCCGTGGAAT
EST: gi|86036710|gb|DR332465.1|DR332465
EST:     AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAA                         ACATATCTTTTACCAGATTCTCCGTGGAATTGCGTATTGGCC-CTCTCATA
genomic: AGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAAgtgagtgcta ... ctattttcagACATATCTTT-ACCAGATTCTCCGTGGAATTGCGTATTG-CCACTCTCATA
EST: gi|125285419|gb|EL299504.1|EL299504
EST:     ATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAA                         ACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGG
genomic: ATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAAgtgagtgcta ... ctattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaactcaatactcaatataagctgatcagagctgttcatccactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA
                      agctgat  putative branch site (score: 4)
                                             ctattttc  putative PPT
         aatactcaatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcatccactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC