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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgatttccttaacag

Basic information

species Glycine max
transcript GLYMA04G39520.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 4
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgat---ttccttaacag
 || ||||| ||||||||  | |||||||| | ||||||||||||||| || || || ||||  || | ||| ||||||||||| ||||||||| ||||      ||| | ||  |   |    ||  ||  |   |  ||  |     |  | ||   ||| |  |||||   ||  ||     |  || || |||  | |    ||| |   |||
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGC------Tgtaagttcaagctgcactata-atcatggcacacagttacatctactata-accacca--tagtg---ttgtcttcgcatctacata-atgtctaacaagttcatcctcag

upper sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 4
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgatttccttaacag
 || || || ||||||||||| |||| |||||  ||||| || || ||||||||||||||  | || ||||||||||| ||| | ||||||||| |||| || ||  |   | ||   |   |     | |||  |    | | ||  || || ||| | |    |||   |  |    || ||||     |  || || |             
TGTCGAAATCGAGAGAGCTCGTTTGACCAAGATGCTTGCTAAGATTAAGGAAGAACAAGGTTTGATTGCTGAAGCTGCGGATCTCATGCAAGAAGTTGCTgtaagctt--ttcttcctctactttccaactttcgtggaaatcgttttttatt-tattttatagtttatcaatgtgcattgattgtgattatgaattatag-------------

upper sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 4
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttgg--tttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgatttccttaacag
 ||||| || ||||| || ||  | | |||||||||||| || || ||||||||||| || |  |||||||||||||| ||| | ||||||||| |||| || ||     |||||   | | ||        |||||     | | |   ||||  |   |   ||     || ||||   || |   | | | |||                   
TGTTGAAATCGAGAGGGCACGTCTCACCAAGAAACTTGCTAAGATTAAGGAAGAACAGGGTCAGATAGCTGAAGCTGCAGATCTTATGCAAGAAGTTGCTgtaag-----attttgtgcatttggc------tattaaatctcctggaaattttcttcccttgttaacccctgcaatt---tgataaataattaacag------------------

upper sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 4
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttg-acttaca---tgattgat-ttccttaacag---
 ||||| || ||||| |||||| ||||||||||||| |||||||| |||||||| ||||| | ||||||||| || ||||||||||||||||||||||||||||||   || |  | |  |   ||||  ||| |     |  |||||| || | |   |||||          ||   | | | ||  ||   ||   || ||||| || |||||      
TGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATAAAGGAAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagttaaaaat--agagttaccatgggcttttt-----atttttggtattagaaaa-cactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacag

upper sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 5'ss of exon 4
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaa---ttagctgtttgttgacttacatgattgatttccttaacag-----------------------------------
||||||||| || |||||||| || |||||||| || || || ||||||||||||||||||   || || |||||||| ||||  ||||||||| | |||||   |||||  ||    ||||   | |||    | |        |    | |  ||||   | ||  |  | |   || | || |  | || |     |  || | |  | || |                                    
CGTTGAGATAGAAAGAGCTCGCTTAATCAAGAAGCTAGCGAAGATCAAGGAAGAACAAGGAAACATCGCCGAAGCTGCGGATTGCATGCAAGAAGTCGCGgt--atgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgta-atgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcag

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|208233022|gb|GE032775.1|GE032775
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193674954|gb|FK616072.1|FK616072
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGG
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGG
EST: gi|193411717|gb|FK381652.1|FK381652
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTTGAGAAAATCGCATTCATTCT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAAC-TGAGAAAATCGCATTCATTCT
EST: gi|193430352|gb|FK397288.1|FK397288
EST:     AGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCT
genomic: AGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA-TTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCT
EST: gi|20812745|gb|BQ297231.1|BQ297231
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|207771711|gb|GD742486.1|GD742486
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAAGAAAATCGCAT-CATTCT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGA-GAAAATCGCATTCATTCT
EST: gi|208080953|gb|GD873823.1|GD873823
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAA
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAA
EST: gi|193702744|gb|FK639176.1|FK639176
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|15284713|gb|BI468604.1|BI468604
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193364691|gb|FK330120.1|FK330120
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193530760|gb|FK484523.1|FK484523
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193328951|gb|FK295195.1|FK295195
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193426023|gb|FK390800.1|FK390800
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|192297411|gb|FG990689.1|FG990689
EST:     AAGGACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193627757|gb|FK577939.1|FK577939
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTC
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|208038643|gb|GD834543.1|GD834543
EST:     TGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: TGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|207725740|gb|GD700972.1|GD700972
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|7478560|gb|AW666314.1|AW666314
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|193412299|gb|FK381226.1|FK381226
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|11274759|gb|BF325094.1|BF325094
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgatttccttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA