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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatggttgcctagctttttcttcccttgttacacttgttgacaggatattgctgaacatgcatctatgtgcag

Basic information

species Glycine max
transcript GLYMA13G19500.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 4
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaat-catggttgcctagctttttcttcccttgttacacttgttgacaggatattgctgaacatgcatctatgtgcag------------------------------
||  | || ||    |  || |||||||| ||||||||||||||||| | ||||||||| ||  ||||||  || ||      |  |  ||| ||  || ||  | |     ||   || || |     |  |    ||||   |                              
GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTGgtaaaacaaggcgattcaattgattcatcattttttttagtga--aaccatatttttccagtgactctaaaatgttttgtacatcatttggttgtatgcacatgtaaag

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 5
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaat-catggttgcctagct----------ttttcttcccttgttacacttgttgacag----gatattg------------ctgaacatgcatctatgtgcag
||  | || |||   |  || |||||||| ||||||||||||||||| | ||||||||| || | |||||  ||  ||||  |  ||          | || ||     | || | || ||| |||     |||||              | ||  ||  |  ||||||||
GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAGgtaaagcaatgttgttttcctcccgctgaagtcttattgtgaagctatatttcttgccagttctaatatttactcctttccgtttcaatctgtgtgcatgtgcag

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137930_T03 (Zea mays), 5'ss of exon 3
----------------------------------GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaat-catggttgcctagct----------ttttcttcccttgttacacttgttgacag----gatattg------------ctgaacatgcatctatgtgcag
                                  ||  | || |||   |  || |||||||| ||||||||||||||||| | ||||||||| || | |||||  ||  ||||  |  ||          | || ||     | || | || ||| |||     |||||              | ||  ||  |  ||||||||
AGACTCATAGAAGCGACTCCTATTCCTATGCCAGGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAGgtaaagcaatgttgttttcctcccgctgaagtcttattgtgaagctatatttcttgccagttctaatatttactcctttccgtttcaatctgtgtgcatgtgcag

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgta--atcatggttgc-ctagcttttt---cttcccttgttacacttgttgacaggatattgctgaacatgcatctatgtgcag
||||| || ||||| ||||| |||||||||||||||||||| |||||||  || || || |||| ||||  |   || ||||  || |||| |   ||  || | | |   ||   |  | |||  |    |   | ||  |||   |||
GTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAGgtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcag

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 4
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatggttgcctagc--tttttcttcccttgttacacttgttgacaggatattgctgaacat-gcatctatgtgcag
||||| |||||||||||||| |||||||||||||||||||||||||| | ||||||||| || | |||||| | |  | |  | |  |||||||        |   |   |  |||     ||||| ||  |   ||  ||||||||
GTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAGgtaattaggtgttctaatccatttttctaggtactctttgcagatcaacaattggttgctaaattttatattcatgtgcag

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|298184004|gb|HO029217.1|HO029217
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|12489759|gb|BG043280.1|BG043280
EST:     GGAAGCAAGGTGAAATATTGAACTTGACAAA-GAACCTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: GGAAGCAAGGTGAAATAT-GAACTTGACAAAAGAAC-TGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|26269126|gb|CA820189.1|CA820189
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|192330021|gb|FK020837.1|FK020837
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATGCTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|19346407|gb|BM891287.1|BM891287
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|37996937|gb|CF808526.1|CF808526
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|298181507|gb|HO022946.1|HO022946
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|298169347|gb|HO020707.1|HO020707
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|6133848|gb|AW132241.1|AW132241
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|9565429|gb|BE474938.1|BE474938
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|7587913|gb|AW703719.1|AW703719
EST:     AGGAAGCAAGGTGAAATATGAACTTGANCAAA-GAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AGGAAGCAAGGTGAAATATGAACTTGA-CAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|8403914|gb|BE059548.1|BE059548
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|192324146|gb|FK017877.1|FK017877
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|213593665|gb|DB971687.1|DB971687
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|209719745|gb|BW672120.1|BW672120
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|298178505|gb|HO024240.1|HO024240
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|209701982|gb|BW664582.1|BW664582
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
EST: gi|17154018|gb|BM143951.1|BM143951
EST:     AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG                         GTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT
genomic: AAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatgg ... ctatgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATGgtaatcatggttgcctagctttttcttcccttgttacacttgttgacaggatattgctgaacatgcatctatgtgcag

- - - - - - - - AAGGAA
- - - - - - - - - - AAGCAA
- - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - -  AAGAAC