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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT

Basic information

species Arabidopsis thaliana
transcript AT5G65960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g49530.1 (Oryza sativa), 3'ss of exon 4
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                                          |   || | ||||     | |       ||    ||   | ||    |  | ||    | ||   ||| |||    | | | |    |  |  |||       ||||| |||| ||  |||| |||  ||||||  | || || ||  |||| || ||||| || || ||||||||||| |||||||||||||||||  | || ||
--------------------------------------------------------------------------aatctccaatgaaa--aaggacttgttctggccaaagtcgaatatttactggatgttggaatgtttctttcttaattgacttatatccgtgccttg----caatagGTCTATCGGTGAATGGAGATAGTCAAGGCTTAGAGCGACTCCTTGGAGCCCTTTCTGCACACATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G700662_T01 (Zea mays), 3'ss of exon 7
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgag--cagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                              |  || |   || |            |  |  | | |     |  ||| | || | |   || | |  |   ||  | || ||| |   |||  ||| | | |    ||    ||   ||||  |||||| ||||| |||   |||||  | || || || ||||| |||||||| || |||||||||||||| |||||||||||||||||  | || ||
-------------------------------------------------------------gtgatcttcacatgggcggagggagtatcttttagggactccaatagaagaaggcttatatcatataggaattgtggttgtttctatcttatt--tgatgttta----ttcaaactaacagGTCGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G386125_T01 (Zea mays), 3'ss of exon 8
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                                   | |    ||  |||  |         |||  ||   |  | | |    ||  |     |||    ||  | || ||| |   |||  ||| | | |    ||    ||   || |  |||||| ||||| |||   |||||  | || || || ||||| |||||||| || |||||||||||||| |||||||||||||||||  | || ||
------------------------------------------------------------------gcatagggagtatcttttagggactccaatagaagaaggcttatatcatatagg-----aat---tgtggttgtttctatcttatt--tgatgttta----ttcaaactaacagTTAGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G314386_T01 (Zea mays), 3'ss of exon 4
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                                  |  || | | ||| ||      ||  | |    ||  ||   | || | ||   |||    ||  |||  | || ||| |  | | | ||| | | |    ||    ||   |||| ||||||| ||||| |||   |||||  | || || ||  |||| |||||||| || |||||||||||||| |||||||||||||||||  | || ||
------------------------------------------------------------------caatgaa-aacttatatcttttttagggactccaataga---agaaggcatatacag----taaccgtggttgtttctat--cttaattgatgttta----tttaaactaacagGTCTATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCCTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT

upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G32900.1 (Glycine max), 3'ss of exon 4
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                                  | |  |  | ||| | |||  |||   ||   ||  | ||   | |  ||||| ||  | | |    | |||   | |         ||||   ||||    |  |  ||  ||| || ||  | ||||| ||||  ||||| ||||| ||||| |  ||||| ||||| ||||||||||||||||| ||| |  |||||||||| ||||||||
-----------------------------------------------------------------ccatattcaaactttttctg--cttaccaa---aacttaaggatataatgatgaacattggaaaattattttcagatat---------atgattttcacacaattatt-ttacagGCTTGTCCATAGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGAT

upper sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g02260.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttctatctccttccttctgattatatattgactgcaatatgcccaatgtaatctggttactccttgtatagcttctactgaacttgtgaatgaaaagtgagtgaaaatggatgagcagagaatacgcgtattcgtctctctagcattaatg-aggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                                                            |||| ||   | |     |  ||   |  ||      | | |||        |    | ||| | | ||   |||  ||  |     || || || || |   |||||| |||||  |||| ||||| ||||| |||||  |  |  | ||||| ||||| ||||||||||||||||| ||||  |||||||||||||||| |||
---------------------------------------------------------------------------ccttcaacactattctcccacaaagtttaggtcttg--gaaagagtt----ccatttttcttcctttttcggtcatccatttatataaactggctgttcatgacagGTTTGTCAGTTAATGGTGATTCACAAGGAGTTGATAGAATCCTGGGTGCACTTTCTGCTCATATGTGGCCTGGAATGACCCTGAAATCTGGTGATAAGAT

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|124833253|gb|EH917692.1|EH917692
EST:     TAACATTGAGTTCATTGAGGCTTGTGCCTCTAATCCTGATTTTGACAAGT                         GTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGT
genomic: TAACATTGAGTTCATTGAGGCTTGTGCCTCTAATCCTGATTTTGACAAGTgtaagttcta ... gtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacgcgtattcgtctctctagcattaatgaggctcacgggttggtccttgtagGTTTATCAGTCGATGGGGATTCTCAAGGGGTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGAT
                                ggctcac  putative branch site (score: 3)
                                              tccttgt  putative PPT
                        attaatga  TA-rich tract