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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
gtatgtttcatgaccagtg-atgatgttgattcactgattcatattctcatgtcaattataactctc-ttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
|||  ||  | || || |  |     || |  |||| |   ||  | |    | ||||||   |||  ||||||||||||||||    ||||||||||| ||||||||||| ||||| || | ||| || || |||||||||||||| ||| | ||  | || |||||||| ||
gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
||   ||  |         |  ||| |||||      || ||    | ||     | ||       |||||||||| |||||   |||||||||||| ||||| || || |||||||||| |||||| || |||||||||||||||||| | ||  | || |||||||| ||
gttaattcaaaacgtcagaagaatggtgattt--cagtttattagttaatacgtttcatg------ttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 2
gtatgtttcatgaccagtgatgat--gttgattca-ctgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
|||  || ||  ||    || |||  || | ||||  | ||| ||    |  |  |||         | |||||||||| |||||   |||||| ||||| ||||| || || ||||| |||| ||||||||| |||||||||||||||||| | ||  | || |||||||| ||
gtaaattccaaaacatcagaagattggtggtttcagtttatttatgagttact--caacacgtttcttgttgcagGTATTCAAACCTCCGAGGATTACAGGTTCTATGCCATTTCAGCCGAATACCCTGAGTTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 2
--------------------------------------------gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
                                              |||||| ||     |  |  ||    ||| |   ||   | || |    | |||  | |      ||||||||| ||||| || ||||| ||||||||||||||||| |||||| | | |||||| || |||||||||||||||||  ||||||||||||| ||||||||
gtaaactaaattgctatattgaacagtcttgtattatttcttgctcatgttt-atttttggctaaaattgatattaagatatgtttgtttttggctgaatgttgatatctatgcagGTATTCAAACCAGTGAGGATTACAGATTCTACGCTATTTCAGCTCAGTACCCTGAATTCAGCAACAAGGATAAGACACTAGTCTTCCAATTTTCTGTCAA

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 2
--------------------------------------------gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
                                             | |   |||||   | |  || |    ||| |       ||||  |    | |||  | |      ||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| | |||||| || |||||||||| ||||||  ||||||| ||||| ||||| ||
gtaaactaaattgctatgttgaatagtcgggtattatactattattgttgctcatgtttacttttgtttaaaattgatattaagatatgtttggttgaatgttgatatctctgcagGTATTCAAACCAGTGAGGATTACAGATTCTATGCTATTTCAGCTGAGTACCCTGAATTCAGCAACAAGGGTAAGACACTAGTCTTTCAATTTTCTGTTAA

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaatt--ataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
                                       |||||||||   |  |  | || | || |     ||   ||   | || | | ||  ||        |  |||||||||||| || ||||||||||||||||| |||||||||||||| | |||||| || |||||||| |||||||| ||||| ||||||||  |||| ||
gtattattttcatacacattcttatacctatttggggcaatgtttcattctctttattaatttggactttgaaatgtgtaacttgatttgacttcaatggtctggatatagGTATCCAAACAAGTGAGGACTACAGATTCTATGCTATATCAGCTGAGTACCCTGAATTCAGCAACAAAGATAAGACATTAGTTTTCCAATTTACTGTTAA

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|86070958|gb|DR366715.1|DR366715
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070961|gb|DR366718.1|DR366718
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070960|gb|DR366717.1|DR366717
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|116465716|gb|EG508308.1|EG508308
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|125233746|gb|EL247831.1|EL247831
EST:     TCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: TCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|116465698|gb|EG508290.1|EG508290
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070962|gb|DR366719.1|DR366719
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070954|gb|DR366711.1|DR366711
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070959|gb|DR366716.1|DR366716
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070953|gb|DR366710.1|DR366710
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070957|gb|DR366714.1|DR366714
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|86070956|gb|DR366713.1|DR366713
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|116482409|gb|EG525001.1|EG525001
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
EST: gi|116465734|gb|EG508326.1|EG508326
EST:     GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAG                         GTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC
genomic: GGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAACGATAAAGgtatgtttca ... tctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA
                                      ttataac  putative branch site (score: 2)
                                            ctctcttgc  CT-rich tract
                                  tcaattataa  TA-rich tract