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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC

Basic information

species Arabidopsis thaliana
transcript AT4G14350.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 3
gtatttaaattccttcaagtggctttcgtt-------tgacatttgtttagttggttgatgtgaatgtggaatctgatt-ttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
||    ||||       | | ||| || ||       |||   |||| | |||   |    ||  |      | |   | || |||| |||||||||||||| ||||| ||| ||||||||||||||||||||||||||||||| || || |||| ||| || ||||||||||||||||| ||||
gttacaaaatcatcaggacttgctctcattgttaaaatgaatattgtcttgttaaattcattggttactttctatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGATAGCAATTGCATTGTAAAGCTTTATTATTCCTTTCAAGATGAAGAGTACTTATATC

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
     | || |  |   | ||        ||    |   | | |||   | || || ||  |  |     ||||||||| |||||||| ||||| ||||||||| ||||||| |||||||| |||||||||||||| ||||| |||||||| || |||||||| ||||| || ||||
----gtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 4
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
     | || |  |   | ||        ||    | | | | |||   | ||    || ||||  |  | |||||||| |||||||| ||||| ||||||||| ||||||| |||||||| |||||||||||||| ||||| |||||||| || |||||||| ||||  || ||||
----gtgaaattatcacattgttagagacttagtgtatatattgttttcttatacttat-tggatac--actttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTAAAACTTTATTGTTCCTTTCAAGATGAGGAGTTTTTATATC

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgatt--------ttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
|||   ||||       | | ||| || |||   |  ||  || |   ||| | |     | || |    ||        || |||| |||||||||||||| ||||| ||| |||||||||||||||| ||||| |||||||| || || |||||||| || |||||||||||||| || ||||
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
---------gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
          | ||    |  |    | |   ||  || | | |||| |||   |  |||      || ||     | || || |||| |||||||| || || ||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||
gtatgacttctgttggcctggcagacaatttattgtgtgttatatttatttttcttattgcc--cgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------------------------gtatttaaattccttcaagtggctttcgtttgacat---ttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
                                                                                                                         || ||   | ||  |  |||        | |||      ||  ||      || |  | ||||   || |    || |||||||| |||||||| |||||||||||||| |||||||| ||||| || || ||||| || ||  | ||||| || || ||||| ||  ||||||||||  
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccatttta-atcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------gtatttaaattccttca-agtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
                      | ||  || ||| |    |||     |  |    | | |  |||      || | | || |     |    ||  ||||| || ||||| ||||||||||||||| |||| || |||||||| ||||| || ||||| ||  |||||||||| || ||||| || || ||||||||  
ccgttgttttcatgcttgatatgcatacaagttcttagggagtttaccttatccttcttgtacttaaccatgtgctttcaacgcaacgtggtcttggcagGTAGAGCATGTTAAAGCAGAGAGAAATCTACTCGCTGAAGTTGACAGCAACTGTATTGTGAAGTTGTATTGTTCATTTCAAGACGAGGATTACTTGTACT

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------gtattta-aattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
                        || | | || |  ||  |  | || |  |     |      |||    ||||  ||||  |        | || |||||||| ||||||||||||||||||||||| |||||||| || ||||||||||| ||||| ||  ||||||| || || |||||||| ||||| |||||| 
tcatcataagaatgataacaataataatgataaatatttttatcgactatgatagtgaaaaatcatagcca-ttgaattgaaaattttgcggtaattgcagGTGGAGCATGTAAAAGCAGAGAGAAATTTGCTTGCAGAGGTCGATAGCAATTGTATTGTGAAGTTGTATTGCTCGTTTCAAGATGAGGAGTATTTGTATT

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|47828550|gb|CK118234.1|CK118234
EST:     TCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAG                         GTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAAT
genomic: TCTATGCAATGAAGAAGCTTAAGAAATCTGAGATGCTTCGCAGAGGCCAGgtatttaaat ... tgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
                                          atctgat  putative branch site (score: 4)
                                                ttttc  CT-rich tract
            atttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgattttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA