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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgacattgcttatccgatttctaacgcagtaaagtggaatctcgatgtatctatgtactatctagtgttttaatggttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT

Basic information

species Arabidopsis thaliana
transcript AT2G27450.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G31100.2 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------gtgtgacattgcttatccgatttctaacgcagtaaagtgga-----atctcgatgtatctatgtactatctagtgttttaatggttggatggtttaattt----aacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT
                                                                     ||  ||  |  |     | |||     ||||   |    |        | |   | | | || |  |||  ||  |  |     |   || || ||| |     |  ||| |||||||| || ||||| || || |||||||| ||||| ||||| ||||||||||||||||| | ||||||||| ||||| || || ||||||||| ||
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatgaactggaaccgtattatggtgttttaaggggcagaggaacaaatattggcttagtcttttatgtgcatcatcctgtaatgaatcttattcttgtttcaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTTTGAGGAGGCAAACAATGCACATTATAATTCAATAGCCATAATTGATTCT

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------gtgtgacattgcttatccgatttctaacgcagtaaagtggaatctcgatgtatctatgtactatctagtgttttaatggttggatggtttaattt----aacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT
                                                                            | | |  |||||  |   |     |  | |  |||        | |   | | |    |  |||  ||  |  |     |   || || ||| |    ||   ||||||||||| || ||||| || || |||||||| || || ||||| ||||||||||||||||| | ||||||||| || || || || ||||||||||||
gtaaaataattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataaggttgct-gtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTTTGAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCT

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
-------------------------------------gtgtgacattgcttatccgatttctaacgcagtaaagtggaatctcgatgtatctatgtactatctagtgttttaatggttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT
                                      |  | || |||||    |      || | | |  |     ||   | ||     | | ||  |  |    | | ||  ||   ||  |     | |  ||| |||||||| || ||||| || || |||||||| ||||| ||||| ||||| ||||||||||| | ||||||||| ||||| |  || ||||||||||||
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------gtgtgacattgcttatccgatttctaacgca-----gtaaagtggaatctcgatgtatc----tatgtactatctagt--gttttaatg---gttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT
                                                              |||   | |  |  ||  |||| ||  |||       |||  |  |||| ||  |        || ||| || || |    || ||     |||| |    |  ||   |  ||||||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||| | ||| ||||||||||| ||||| ||| ||||||||
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT

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|164225936|gb|EL985076.1|EL985076
EST:     GCCAAGCCTTACAAGAACCATCCTACCATTGCAAG                         GATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGCTTCTT
genomic: GCCAAGCCTTACAAGAACCATCCTACCATTGCAAGgtgtgacatt ... tttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTT
EST: gi|125243157|gb|EL257242.1|EL257242
EST:     GACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG                         GATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGAT
genomic: GACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAGgtgtgacatt ... tttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGAT
EST: gi|125211290|gb|EL226244.1|EL226244
EST:     CCTACCATTGCAAG                         GATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTT
genomic: CCTACCATTGCAAGgtgtgacatt ... tttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTT
EST: gi|124961650|gb|EL036152.1|EL036152
EST:     GACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG                         GATGCAGAAGCTGGCAAAAGGAATTGGGTGTTAGTGATA
genomic: GACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAGgtgtgacatt ... tttaacacagGATGCAGAAGCTGGCAAA-GGAATTGGGTGT-AGTGATA
EST: gi|164101876|gb|ES064870.1|ES064870
EST:     GAC-TCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG                         GATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATAC
genomic: GACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAGgtgtgacatt ... tttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatctatgtactatctagtgttttaatggttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT
                                            atttaac  putative branch site (score: 3)
                                    atggtttaatttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgacattgcttatccgatttctaacgcagtaaagtggaatctcgatgtatctatgtactatctagtgttttaatggttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG