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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattcttctcttggtttgttctgttattgctgaatacttgtatatacagttcatgagttatcttgaaccttgtgatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G11860.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G11860.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G00710.1 (Glycine max), 5'ss of exon 2
GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattcttctcttggtttgt--tctgttattgctgaatacttgtatatacagttcatgagtt-atcttgaaccttgtgatgcag---
 ||| ||||||| ||||| || || |||||||| |||||  ||||||| |||||||| || ||||| ||||| || ||||||||||||||||| || |||||      || | ||  || | |  |||  |  |      || ||    || |      |||   ||| |    || || |  |   |  |||   ||   
AGATCTGGCTCATATTGAGGAGCATATGAAGGCATTCAAGGCCAAAGGTGGTGATGTGTCATGGCACATCCATGATGAGAGATCTCTTCTTGCTCTGCAGgtc-atttatcaaaatgttgtgcatttgcatcatgacacatttttaaaaaacatgctgctattgggtttaccccttcatttccatattattgagatagctg

upper sequence: AT1G11860.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G01550.1 (Glycine max), 5'ss of exon 2
GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattcttctcttggtttgttctgttattgctgaatacttgtat---atacagttcatgagttatcttgaacct-tgtgatgcag-------
 ||| ||||||| ||||| ||||||||||| || |||||  ||||||| |||||||| || ||||| |||||||| |||||||| || ||||| || |||||     |||| ||  |  ||  |||   ||       |   |||| |||||     |   |     ||  |  ||||| |   |||  | |  ||| |       
AGATCTGGCTCATATTGAGGAACACATGAAAGCATTCAAGGCCAAAGGTGGTGATGTGTCTTGGCACATCCACGATGAGAGATCCCTACTTGCTCTGCAGgt-----catt-tagaacgctcttctacattgacatcatgcatgctaaatacacaccttcaacttgttttgtttgttatgtattaccgatttcctgctgtttctga

upper sequence: AT1G11860.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G11590.1 (Glycine max), 5'ss of exon 2
GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattcttctcttggtttgttctgttattgctgaa--tacttgtatatacagttcatgagttatcttg--aaccttgtgatg-cag-
 ||| ||||||| ||||| ||||| |||||||| |||||  | ||||| |||||||| || ||||| ||||| || |||||||||||||||||  | |||||      || | |   || | |  |||  |  |           ||||  ||||  |||  |   | | |     | ||||  |   |||||||| | | 
AGATCTGGCTCATATTGAGGAACATATGAAGGCATTCAAGGCAAAAGGTGGTGATGTGTCATGGCACATCCATGATGAGAGATCTCTTCTTGCTTTGCAGgtc-atttatcacactcttgtacatttgcatcataacacacactttgaacttactgctattgagtttacctcctccaacttggtattattgtgatggctgt

upper sequence: AT1G11860.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv10s0116g01540.t01 (Vitis vinifera), 5'ss of exon 1
GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattct---tctcttggtttgttct-gttattgctgaatacttgtatata-cagttcatgagttatcttgaaccttgtgatgcag--
||| ||||| |||||||| || || |||||||||| ||| |||||||| || || ||||| ||||||||||| || ||||| |||||||| || || |||||        |  |||| |||   |  | | |   ||||| ||| |     | |  |    |  | || |||  ||||  |  |   |  |  |    ||  
GGACTTGGCCCACATTGAGGAGCATATGAAGGCTTACAAGTCCAAAGGCGGGGACGTCTCATGGCATATCCATGATGAGAGGTCTCTTCTAGCTCTCCAGgtc--atttctcaaagactctgaattccattgagagttctagttgtaatatacttttcacctgcagcaattctagagtatttcttttcagttggtcagagta

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|125079060|gb|EL141209.1|EL141209
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACA
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACA
EST: gi|125268287|gb|EL282372.1|EL282372
EST:     TCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAAGAAAGACTTGA
genomic: TCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAA-GAA-GACTTGA
EST: gi|124949036|gb|EL024707.1|EL024707
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAA
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAA
EST: gi|125184453|gb|EL199407.1|EL199407
EST:     GAGAGATCTCTTCTTG-CCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: GAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|164191447|gb|ES022908.1|ES022908
EST:     CCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGAC
genomic: CCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGAC
EST: gi|125262497|gb|EL276582.1|EL276582
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTG
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTG
EST: gi|124786384|gb|EH876063.1|EH876063
EST:     CTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: CTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|124771198|gb|EH861328.1|EH861328
EST:     TGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGACCCTTCAG                         GGTCCTTTGGCTGCTCCAGTG
genomic: TGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTG-CCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTG
EST: gi|124958907|gb|EL033618.1|EL033618
EST:     CATATCCACGACGAGAGATCTCTTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: CATATCCACGACGAGAGATCTC-TTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|124841734|gb|EH926171.1|EH926171
EST:     TGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTACTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCA
genomic: TGATGTCTCGTGGCATATCCACGACGAGAGATCTCTT-CTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCA
EST: gi|125019285|gb|EL091554.1|EL091554
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCT
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCT
EST: gi|47832124|gb|CK121808.1|CK121808
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|47832114|gb|CK121798.1|CK121798
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|124757126|gb|EH847256.1|EH847256
EST:     CTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: CTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|125229820|gb|EL243905.1|EL243905
EST:     TCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: TCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|47829607|gb|CK119291.1|CK119291
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTNCA-CACCTGACTAAAGAAGACTTGAG
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTT-CAACACCTGACTAAAGAAGACTTGAG
EST: gi|116483791|gb|EG526383.1|EG526383
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|164044632|gb|ES148071.1|ES148071
EST:     GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAAC
genomic: GTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAAC
EST: gi|124704748|gb|EH796150.1|EH796150
EST:     AGATCTCTTCTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: AGATCTCTTCTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
EST: gi|125187425|gb|EL202379.1|EL202379
EST:     CTTGCCCTTCAG                         GGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC
genomic: CTTGCCCTTCAGgtttggccat ... tgtgatgcagGGTCCTTTGGCTGCTCCAGTGCTTCAACACCTGACTAAAGAAGACTTGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATTTGGCTCACATTGAAGAACACATGAAGGCTTTCAAATCCAAAGGAGGTGATGTCTCGTGGCATATCCACGACGAGAGATCTCTTCTTGCCCTTCAGgtttggccattataagattcttctcttggtttgttctgttattgctgaatacttgtatatacagttcatgagttatcttgaaccttgtgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC