Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaggcattctactttttccttaagttatgacattaattattggccactaatttcatgttacaatttagttgctgatttgaaaatctctttcatttaattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCAAGAAAGATTAGTACGAGAGTGTTTGATGCTGATGTTTCAAAGGAAAAGA

Basic information

species Glycine max
transcript GLYMA04G39520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------gtactaggcattctactttttccttaagttatgacattaattattggccactaatttcat------gttacaatttagt--tgctgatttgaa---aatctctttcatttaattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCAAGAAAGATTAGTACGAGAGTGTTTGATGCTGATGTTTCAAAGGAAAAGA
                                           | |     || || | ||   |||| |  |   |  | ||||| |  ||| |||| ||      |||  || ||  |  ||||  |||  |   |||    || |  | | | | ||||| ||  ||||| |||||||||| |||||||||||||||||||| |||||||| ||||| ||  |||| || || |||||||||  |||||| |||||||
gtacgtgttatcttctttcattgttcttttaattacttctaccatttattcttttattgttcttttaattacttgtaccatttattcgtaacttattttatttttgggttcaaagttgataatgctactttttatgtaataatgttgaaattacttttcagGTCCGGCTGTGTTTAGACCGCCAAGATTATGTTCGTGCACAAATTCTCTCAAGGAAGATCAGCCCGAGGGTTTTCGATGCTGATTCTTCAAAAGAAAAGA
















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:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCG
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCG
EST: gi|193411717|gb|FK381652.1|FK381652
EST:     TTTTGGTGCCATGGCTAAAACTTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: TTTTGGTGCCATGGCTAAAAC-TGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193430352|gb|FK397288.1|FK397288
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|20812745|gb|BQ297231.1|BQ297231
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|207771711|gb|GD742486.1|GD742486
EST:     TTTTGGTGCCATGGCTAAAACTGAAGAAAATCGCAT-CATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: TTTTGGTGCCATGGCTAAAACTGA-GAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193702744|gb|FK639176.1|FK639176
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|15284713|gb|BI468604.1|BI468604
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193364691|gb|FK330120.1|FK330120
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193530760|gb|FK484523.1|FK484523
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193328951|gb|FK295195.1|FK295195
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193426023|gb|FK390800.1|FK390800
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|192297411|gb|FG990689.1|FG990689
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|7478704|gb|AW666372.1|AW666372
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|193627757|gb|FK577939.1|FK577939
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTCGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|208038643|gb|GD834543.1|GD834543
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|207725740|gb|GD700972.1|GD700972
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|7478560|gb|AW666314.1|AW666314
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATAGCTCTC
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATA-CTCTC
EST: gi|193412299|gb|FK381226.1|FK381226
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
EST: gi|11274759|gb|BF325094.1|BF325094
EST:     CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA                         GTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA
genomic: CTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAAgtactaggca ... aattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgttacaatttagttgctgatttgaaaatctctttcatttaattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCAAGAAAGATTAGTACGAGAGTGTTTGATGCTGATGTTTCAAAGGAAAAGA
                                   tctttcatttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaggcattctactttttccttaagttatgacattaattattggccactaatttcatgttacaatttagttgctgatttgaaaatctctttcatttaattgtgcagGTTCGTTTGTGTCTAGACCGCCAGGATTATGTTCGTGCACAAATACTCTCAAGAAAGATTAGTACGAGAGTGTTTGATGCTGATGTTTCAAAGGAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA