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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggttacttaagtgctattttgtgttcatttcactttgatcttttgttcaaaaattttagatatctcacaccaatttcttgcccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG

Basic information

species Arabidopsis thaliana
transcript AT1G14810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 4
---------------gtgagtggttacttaagtgctattttg-tgttcatttcactttgatcttttgttcaaaaattttagatatctcacaccaatttcttgccc-----ttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG
                |   ||  ||   |     |   ||  | | |||   |||||  |||||   |  || |    | | ||  ||  | || ||  |||       |||  ||||||| | ||| || || ||||| ||||| || ||||| ||||| || |||||||| ||||| || ||||||||||| |||||||| || || |||||||
gtatgtgaaagccaaattgatgtctaggaagtcattgcattactctccatccaacttttctctttaactttaagaaaacataaattacatcctaactttatgcttctctattcctagAATGATAAAGATGTGAAGGTAACTGCAACCTGCATACGAGTTCCTGTGATGCGTGCACATGCTGAAAGTGTGAATCTACAGTTTGAAAAGCCACTTGATG

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05250.1 (Glycine max), 3'ss of exon 4
gtgagtggttacttaagtgctat-tttgtgttcatttcactttgatcttttgttcaaaaattttagatatct--cacaccaatttcttgcccttc-acagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG
||| ||     || || |   || ||| |      || | |  | | |||||||  |   | |   |||  |   |         ||||| |||| ||||||| | |  || || |||||||| || || || ||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||| |  || |||||||
gtgggtaa--gctgaaattgaatctttataaattgtttattaggtttttttgtttcatgttatggaatagttgctaagttttacccttgcacttctacagAATAATAAGGACGTTAAAGTAACTGCCACATGCATACGAGTTCCTGTCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAACACCCCTTGATG

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 4
gtgagtggttacttaagtgctattttgtgttcatt-tcactttgatcttttgttcaaaaattttagata-tctcacaccaatttcttgccctt-cacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG
||| ||    ||| || |   || || | |  ||| |   || | | |||||||  |   | |   ||| |  |  |      |||||| |||  |||||||||||  || || |||||||| || || || ||||| |||||  | ||||| |||||||| ||||||||||||||||| ||||| |  || |||||||
gtgggtaa--actgaaattgaatctt-tataaattgtttattaggttttttgtttcatgttatggaatagttgctaattttactcttgcacttatacagAATGACAAGGATGTTAAAGTAACTGCCACATGCATACGAGTTCCCATCATGCGAGCTCATGCTGAGAGTGTGAATCTTCAATTTGAAAGACCCCTTGATG

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------gtgagtggttacttaagtgctattttgt----gttcatttcac-----tttgatct---tttgttcaaaaattttaga---tatctcacaccaatttcttgccct---tcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG
                                 |   ||||||  ||  | ||  ||||     |||  |||| |      | |||        | ||  || || |  |   ||| | |||  | ||| |    ||   |   |||||||||   | || ||||| || || || || ||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||
gtgagtttatgatcttttattccttgctcttcatatttggttaactagatacttctttgatagggtttgtttcgcagatgctggataggagccaggtcttaatttgtgtagtttatataacatgactttttgtttctatgttgtagAATGACATGAATGTTAAAGTGACTGCCACATGCATACGGGTCCCTGTTATGCGTGCGCATGCTGAGAGTGTTAATCTCCAGTTTGAGAATCCCCTTGATG

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|116453473|gb|EG496065.1|EG496065
EST:     GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG                         AATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
genomic: GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGGgtgagtggtt ... cccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
EST: gi|116396484|gb|EG439076.1|EG439076
EST:     GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG                         AATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
genomic: GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGGgtgagtggtt ... cccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
EST: gi|116453474|gb|EG496066.1|EG496066
EST:     GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG                         AATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
genomic: GTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGGgtgagtggtt ... cccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
EST: gi|86083642|gb|DR379401.1|DR379401
EST:     GAGACAAGGAAGATCTGG                         AATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG
genomic: GAGACAAGGAAGATCTGGgtgagtggtt ... cccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcttttgttcaaaaattttagatatctcacaccaatttcttgcccttcacagAATGACACAGAAGTAAAAGTAACAGCAACGTGTATACGTGTTCCAGTTATGCGTGCTCATGCAGAGAGTGTGAATCTTCAGTTTGAGAATCCTCTTGATG
                          atctcac  putative branch site (score: 3)
                                      tttcttgcccttcac  putative PPT
     ttttgttcaaaaattt  TA-rich tract