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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC

Basic information

species Arabidopsis thaliana
transcript AT4G01720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G092694_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaatt------gaatcaatattaatatataa-tatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                                                                       | |   |||| | |||  || ||||    |  |  |||      |  ||  || |   |  | ||  ||      | || ||| |  |||| ||  ||||| | |  ||||| |||||||||||||| ||||| ||||| ||||| ||||| || ||||| ||  | || || || || ||||| ||||| || | ||| |
gtacgcatgggactggtatggaatagaggggaagcctgggaattaaagtgttagttgtttctcattcattattgctcgacgatcatatgaacatctaaaggtt-ttatttttaaaaagacaattatttcatccaattaatgtacatactaaagtttttttatgcatgaatttgtatatttatctatagATCAGCGACGGGTGTCAATGGAGAAAGTACGGGCAGAAGATGGCCAAAGGTAACCCATGCCCAAGAGCATACTACCGGTGCACAATGGCTGTGGCATGCC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G27860.1 (Glycine max), 3'ss of exon 7
-------gtaactttcta-taagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
           ||  ||| | |  ||  |||||      ||    |   || |   |   ||||   || || ||  | ||| ||| |  ||  ||  |  || | |  || |||||||||||||| ||||| || || ||||| || || || ||||| ||||| || || |||||||||||||| |||||||| ||||| |
atataataaggctacctaattaaatataaatttccccagttaaaatctactaatccacgcatattt-ttgtgtaatat-aatgaatgtgcattaatttt-cagATTAGCGATGGATGTCAATGGAGGAAATATGGACAAAAAATAGCCAAGGGTAATCCTTGTCCCCGTGCCTATTATCGTTGCACTATGGCCGTAGGATGCC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G01030.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtaactttctataa-gttactaatttttttga-------ttcgtttaaccttacatatatatatgagttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                                       |||| ||  ||||| | |||| | ||   | |       | |  ||||   |||  ||  | |  | ||||    ||  ||| ||| |  ||  ||  |  || | | ||| |||||||||||||| ||||| || || ||||| || || || ||||| ||||| || || |||||||||||||| |||||||| ||||| |
gtaatgattaaatttattttaattatatgtcttaatttatactattgcatattatgtaaattgatataacgctacttaattaaataaaaatttctccagttaaatctactaatccacac-atttatatgtatataatgaatgtgcattaatttt-cagATTAGTGATGGATGTCAATGGAGGAAATATGGACAAAAAATAGCCAAGGGTAATCCTTGTCCCCGTGCCTATTATCGTTGCACTATGGCCGTAGGATGCC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaattgaatcaatatt----aatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
     | | ||  |  || ||| |    |    | | |||  ||  |  |  |||| |   |||    |||| | ||||||     |  | |  |  || |||  || |||||||||||||| ||||| || || || ||||| || || || || || ||||| || || ||||| ||||||||||||| |||||| |
----gtatgtaataactaataaatgcactataccatctaat-ttgtagttgcatatcatgcatgg---ttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatg-agttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                  | ||| |      ||||       |  |||  | ||| |  ||| |     | | |   ||| |   || | |  ||  || |||   |  |  || | || |||||||| || ||| | || ||||||||||| ||||| ||||||||||| |||||||| || || || ||||||||  | ||   ||| || |
gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgt-gttgacgcttgccagcgtttgttcggttctatgaagtaa--caccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S246_89V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaat---tgaatcaatat--taatatataatat----agGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                | ||      |    | |  |||| | | |||    | ||     ||   |  |||  | || || |   || || || ||  | | ||||  | |    || | || |||||||| || ||||||||||| |||||||| ||||| ||||||||||| || |||||||| ||||| || |||||  |      ||| ||||
gtgagaacttggagttctttaaatacttcaacagctactctcatcgcattgcttttgtagcttcaa--agccagctttaagcagttgatatgtgtaagtccctggattaacatggtgagatattttgttttcagATTAACGACGGATGCCAGTGGAGAAAATATGGTCAGAAGATGGCTAAAGGGAATCCTTGCCCTCGCGCATATTACCGCTGCACTGTTATGTCTGGCTGTC

upper sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                    |   || || || | |  |     ||   | | ||| | | |  |  | ||   | ||      |  | |    ||  |  ||| |  | ||| | ||||||||||| || ||||| ||||| |||||||| |||||||||||||| || |||||||| || || || || |||||| | ||    || ||||
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatt-tatctgttttagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC

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|125221733|gb|EL235818.1|EL235818
EST:     CCTATAGAAAAGCTAGGGTTTCCGTTAGAGCTAGATCTGATGCCACTACG                         GTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGG
genomic: CCTATAGAAAAGCTAGGGTTTCCGTTAGAGCTAGATCTGATGCCACTACGgtaactttct ... tataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttacatatatatatgagttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
                                     tattaat  putative branch site (score: 2)
      atatatatatgagtta  TA-rich tract