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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaactgcacgcataaccattttctttccgctctttggctcaatccatttgacagtcaaagacaatgtttaaccagctccgtttgatatattgtctttatgtgtttgttcaagcatgtttagttaatcatgcctttgattgatcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATTCCTCGGTTCTGGACTTCTGCTAGTAAATTATGTTTCAGCCATATCACTA

Basic information

species Arabidopsis thaliana
transcript AT3G11945.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11945.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G113476_T01 (Zea mays), 3'ss of exon 6
gtaagtaactgcacgcataaccattttctttccgctctttggctcaatccatttgacagtcaaagacaatgtttaaccagctccgtttgatatattgtctttatgtgtttgttcaagcatgtttagttaatcatgcctttgattgatcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATTCCTCGGTTCTGGACTTCTGCTAGTAAATTATGTTTCAGCCATATCACTA
                                            |       |   || | ||  |||      |   | |    |   ||| ||    ||  |    ||| | |  |||  || ||  |  ||  ||||           |  ||||  |||||||||||  |||||||||| ||||| || ||||| ||||||||||| || |||||  |  |  ||| ||| ||| || | || ||  |  ||
--------------------------------------------cgtcttcgtattcaattaagaacatcaagaagagaacattctaaaataaatatcattggttgaattgctga--cattctttgt--acaatatcttt--------cccaccagGTATCAAATATCAACTTTGGCAACAAAGCTTGGTGTCAGAAATATTGCATTCCTTGGATCTGGTTTATTATTAGCAAACTATATTGCTGCTATTGCTGTA

upper sequence: AT3G11945.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g07200.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtaactgcacgcataaccattttctttccgctctttggctcaatccatttgacagtcaaagacaatgtttaaccagctccgtttgatatattgtctttatgtgtttgttcaagcatgtttagttaatcatgcctttgattgatcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATTCCTCGGTTCTGGACTTCTGCTAGTAAATTATGTTTCAGCCATATCACTA
                                           |||| |||    | |  | | |    |  ||||     ||| |  |      | ||| ||  | |   |       || |  ||  |||||       |||| | |   ||||||  || ||||||||| |||||||||| ||||| || ||||||||||| || || |||||||||||| |||| ||||||||| ||    |||| |    |
------------------------------------------ttcaaaccaaaccaaaccccatggtgctcattaa-----tccataagcctccctctctctac-tatcaatatcgatctgatatgtgcatcata-----aattgtttt---atagGTATCAGATATCAACCTTGGCAACAAAGCTTGGTGTTAGAAACATTGCTTTTCTTGGTTCTGGACTTTTGCTGGTAAATTATATTGGTTCCATTTTGGCA
















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|125275240|gb|EL289325.1|EL289325
EST:     TGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAAGGAGATCGAAA                         GTTCTAAATATCAACCCTGG
genomic: TGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAA-GGAGATCGAAAgtaagtaact ... tcttgaatagGTTCCAAATATCAACCCTGG
EST: gi|124763249|gb|EH853379.1|EH853379
EST:     CTGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAGGAGATCGAAA                         GTTCCAAATATCAACCCTGGCAACAAAACTTGGA
genomic: CTGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAGGAGATCGAAAgtaagtaact ... tcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGA
EST: gi|164136925|gb|ES188722.1|ES188722
EST:     CTGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAGGAGATCGAAA                         GTTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACA
genomic: CTGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAGGAGATCGAAAgtaagtaact ... tcttgaatagGTT-CCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACA
EST: gi|124952841|gb|EL028080.1|EL028080
EST:     CAAAGGACCTTCCTGATGTTGAAGGAGATCGAAA                         GTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATT
genomic: CAAAGGACCTTCCTGATGTTGAAGGAGATCGAAAgtaagtaact ... tcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgtttgttcaagcatgtttagttaatcatgcctttgattgatcttgaatagGTTCCAAATATCAACCCTGGCAACAAAACTTGGAGTGAGAAACATTGCATTCCTCGGTTCTGGACTTCTGCTAGTAAATTATGTTTCAGCCATATCACTA
                                       gattgat  putative branch site (score: 4)
                    tttagttaat  TA-rich tract