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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

Basic information

species Arabidopsis thaliana
transcript AT2G45290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG
                                                                    |||| |   || || || ||        | || ||||    ||   ||| |  |      || ||||  | | | |||       |||| | |  ||      | ||     ||||||| || ||||||   ||| | ||||||||||| ||||||||||| ||||| ||||| || ||||| || || |||||||  || ||||
--------------------------------------------------------------------aaattc-tggagtgatcggtgaagtgtttaatatggttgacttc--agtttcaa----ctgatttgttcatcgagctt-------gctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG
                                                                            || |||    |  |  |   | ||      ||  |||      |    |||| | |||| | | |   | |  |  ||     |  || | |  |||   |  |||||  ||||  | |||   ||||| ||||||||||| |  ||||| |||||||||||||| |||||||| | ||| |||||||  || || |
----------------------------------------------------------------------------aggttgacatggatgacctttgatggaaatataattgtgaagct----tttaaagttgtgggatc--ttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 1
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagattt-agaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG
                                                                                 | | | | |   ||  | |||| ||  | |   | | |  || ||| | | |||| | | |  | | || |    |   |  || ||   |||   |  ||||| |||||  |||||   ||||| |||||||| || | |||||| |||||||||||||| ||||||||   |||  ||||||  ||||| |
--------------------------------------------------------------------------------aggttcatatggatgacc-tttgatggatatataattgtgaagcttttaaagttgtgggatcttcattagctgaattt--gttgttttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagat-------ttgctgaagcagtgt---tgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG
                                                                                             |  | ||||  | ||||||     ||| || |||     | |   | | | || || |       || |||||    |||   |    |   ||| ||||| ||||| ||||| || ||||||||||||||||| |  || || || || || || ||||||||||| ||||||||||||| ||||||||
-------------------------------------------------------------------------------------------tttatttatttatttatttttctgagctt-agttttgttgctatgagatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG

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|116467576|gb|EG510168.1|EG510168
EST:     GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGG                         GAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACAT
genomic: GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGGgtttgtgttc ... tttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACAT
EST: gi|116464596|gb|EG507188.1|EG507188
EST:     GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGG                         GAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACAT
genomic: GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGGgtttgtgttc ... tttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACAT
EST: gi|116480249|gb|EG522841.1|EG522841
EST:     GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGG                         GAGGAAGATTTGAAGAACTTCCGTCAATGGGGGAAGTAAGACTCCAGGACA
genomic: GCATGTTGCAATACGCTCTGCTTCACCTTGCTGGCTACGACAGCGTTAGGgtttgtgttc ... tttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGG-AAGTAAGACTCCAGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG
                                            ttttttatt  CT-rich tract
                                      ttgaagttttttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC