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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttatgaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA

Basic information

species Arabidopsis thaliana
transcript AT3G22890.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 2
-------------gtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttat--gaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA
              |||   | ||  ||  |  |||| |  ||  | |   |   | |||  | | | |||       ||| |  ||  |    |     |||| || |||||||||||||| ||||| ||||| || ||||| || |||||||| || || ||||| || ||||| || || || ||||||||||| ||||
gcctgtctcccttctaatttatgtagtt--tcattgtctccctagttatcattgatttgttcaacataaaaactcccttgtatcaatttggtctttctttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACCACTGTGGTATCCATATTCCCTTCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 2
-----gtaaaaaaagttatt----gattgttgtgtgtctct--tgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttat--gaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA
      | |   ||||||||    | ||  | ||| || ||  | ||  |   | |||  | |   |||    |  ||| |  ||  |    |     |||| || |||||||||||||| ||||| ||||| || ||||| || |||||||| || || ||||| || ||||| || || || ||||||||||| ||||
tctccctcacctaagttattctgtggtttctttgtctccctaattagcattgatttgttcaacagaaaaactcacttgtatcaatttggtctttctttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACAACTGTGGTATCCATATTCCCATCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------gtaaaaaaagttattgat-tgttgtgtgtctcttgagtgtgagtgtgtgtatcttga-----aatgctaaatgtgtttatgaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA
                                     ||||  ||||||   | ||      |  ||     ||| | ||  | || ||| |     ||| || | |    ||   |||||    ||||| || || ||||| ||||| ||||| ||||| || || ||||| || ||||| || || ||||| || ||||||||||| || ||||||||||| ||||
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgcct-taccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA

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|125245014|gb|EL259099.1|EL259099
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|125230995|gb|EL245080.1|EL245080
EST:     GATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
genomic: GATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
EST: gi|116447940|gb|EG490532.1|EG490532
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116460581|gb|EG503173.1|EG503173
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116460580|gb|EG503172.1|EG503172
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|301501831|gb|HO207371.1|HO207371
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|124859552|gb|EH943989.1|EH943989
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|124923809|gb|EL001961.1|EL001961
EST:     ATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
genomic: ATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGA
EST: gi|125103175|gb|EL157674.1|EL157674
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCC
EST: gi|116453692|gb|EG496284.1|EG496284
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125252837|gb|EL266922.1|EL266922
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|116447947|gb|EG490539.1|EG490539
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125064965|gb|EL132381.1|EL132381
EST:     GGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: GGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
EST: gi|125208677|gb|EL223631.1|EL223631
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|124732049|gb|EH823451.1|EH823451
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTC
EST: gi|124916793|gb|EH990667.1|EH990667
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTT
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTT
EST: gi|116420530|gb|EG463122.1|EG463122
EST:     CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAG                         GTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC
genomic: CAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaag ... tgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtgtgagtgtgtgtatcttgaaatgctaaatgtgtttatgaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA
                          tgctaaa  putative branch site (score: 2)
                                     tttatgaatgtaaaa  TA-rich tract