Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt...

Basic information

species Glycine max
transcript GLYMA01G04570.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g37660.1 (Oryza sativa), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccatt--ttcttttgtttaattaattagtt
||||||||||| ||||||||||||||||| |||||||||||||| || || || ||  || | ||||| || || |||||||| ||||| || || || ||| |||||||   ||  || |  ||||||||||||||   ||||   |          | | |     | ||       |      ||||  |    | || 
TGCGGCGACATCCACGGCCAGTTCTACGACCTCATCGAGCTCTTCCGCATCGGCGGGGACTCCCCCGACACCAACTACCTCTTCATGGGTGACTACGTCGgtaagtttctagctcg-ctacccctctctctctctcttctcctccggcctcggacgcgtgtgttccccttttgggccgatctgcgggtttggtgtggtggt-

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g12580.1 (Oryza sativa), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctct-ctctctctctctata-tatatatattc-cattttcttttgtttaattaattagtt
||||||||||| ||||||||||||||||| |||||||||||||| || || || ||  | || ||||| || || |||||||| |||||||| || || ||| ||||  | |  |   | ||  || | |   | | | | | |||   ||  ||  ||| |  |      |||     |  || || ||   ||  ||    
TGCGGCGACATCCACGGCCAGTTCTACGACCTCATCGAGCTCTTCCGCATCGGCGGCGAGGCGCCCGACACCAACTACCTCTTCATGGGCGACTACGTCGgtcagttcataccccgcgtcctcttcccccctgcgcgcgcgcgctcgattcggtcgatctgtggtggggggattggtgctggctctttttcttttctttc---

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G119546_T01 (Zea mays), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt---
||||||||||| ||||||||||||||||| ||||||||||||||||| || || ||  |||| ||||| || || ||||||||||||||||| || || ||| |||  || |  |  || | | ||     | ||| | ||    ||  | | ||| | |    |   |  | |   |   | |||| | ||   | ||    
TGCGGCGACATCCACGGCCAGTTCTACGACCTCATCGAGCTCTTTCGCATCGGTGGCGACGCGCCCGACACCAACTACCTCTTTATGGGCGACTACGTCGgtcagtccctcc--cgactacgtatcctagcccctcccgcctatcctagccc-ctcccgactcgttcttggttccggtcgatctgttgatttgcatggtggtt

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G133464_T01 (Zea mays), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt--
|| |||||||| |||||||||||||| || |||||||||||||| || || || ||  |||||||||| || || |||||||| |||||||| || || |||  ||  || |  |||   || | ||  || |||| |   |   |||| |    ||| |    |       || |  ||    |   |  |     | |  
TGTGGCGACATCCACGGCCAGTTCTATGACCTCATCGAGCTCTTCCGCATCGGCGGCGACGCTCCCGACACCAACTACCTCTTCATGGGCGACTACGTCGgtgcgtggctacg-cttaccctgccctaactttctcccatgcgg-ctctgttctgctcaacggtttctccccccttgctcacccgcgcagctgtgccgatgc

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctct-ctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt
||||||||||| |||||||||||||| || |||||||||||||| || || || ||  || ||||||| || || |||||||| |||||||| || || |||  ||  || |   | |     || |||| | | || |||  ||    || |  | ||| |     |     ||     | |   |||   | |  |   
TGCGGCGACATCCACGGCCAGTTCTATGACCTCATCGAGCTCTTCCGCATCGGCGGCGACTCTCCCGACACCAACTACCTCTTCATGGGCGACTACGTCGgtgcgtggctacgcttccccgccctgtctcccacgctgctctgtcctggtcccggtttctctccccttgcccgcccgcgccctaactttctctcacgata-

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G10430.1 (Arabidopsis thaliana), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagt--ttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt
|||||||| |||||||||||||| || || || || ||||||||||| || || || |||||||| |||||||| |||||||| ||||| || |||||||||  ||  |||||||||||    || | | | |     | |  || | | | ||||  | || || | | | ||    |   |      |  | ||||  | 
TGCGGCGATATTCACGGCCAGTTTTATGACCTTATTGAGCTCTTTCGTATCGGTGGCAACGCTCCTGATACTAACTACCTCTTCATGGGAGACTATGTAGgtctgtctttcttcttctttcgattttatttttggggtttttact-tttttttctcattttagatctgtgtttttggatcattccaaaatggtgaattctt-

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G59830.1 (Arabidopsis thaliana), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatat--atatattccattttcttttgtttaattaattagtt
|||||||| || || |||||||| || || || || ||||| ||||| || || || || ||||| ||||||||||||||||| ||||| ||||||||||||  || | |   ||||||   || |||| | ||  | |   |             |  || |    || | ||   ||||      | |   |  |||   
TGCGGCGATATCCATGGCCAGTTTTATGACCTAATTGAGCTATTTCGTATTGGTGGTAATGCTCCTGATACTAATTACCTCTTCATGGGAGATTATGTAGgtatgtctttctctcttctctatcactctatttcaattttttttgtgtgggtaagttaaatttcctgatttgttgggtttttagagatctgtgttcttat--

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0026g01080.t01 (Vitis vinifera), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt--
||||| || ||||| || ||||||||||| ||||| ||||| |||||||| ||||| || ||||| || || ||||| || |||||||||||||| || ||| ||||  |   | || |   ||    | | | | |     |     | | | | ||| |    | ||  | |||   |||    | | | |  | ||   
TGCGGAGATATTCATGGGCAGTTCTACGACCTCATAGAGCTGTTTCGGATCGGAGGGAATGCTCCGGACACGAATTATCTTTTTATGGGCGATTACGTGGgtgagttgatagctgttgt--atcaaattttatgtttggttttgggattttttttttctgttgtgacatgattcataagcttgcaatcattgaggtcgtgcg

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S357_57V6.1 (Physcomitrella patens), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt-
||||| || || || ||||||||  ||||||||||||||||||| || || ||||| || || |||||||| |||||||| || |||||||| || || ||| |||| |   ||  | |  ||  |||     | |  |     | |||   ||  |  |  | | | |   ||| |     | |      |  | |    
TGCGGAGATATCCATGGCCAGTTTCACGATCTCATCGAGCTCTTCCGCATCGGAGGCAAGGCGCCCGATACGAATTACCTGTTCATGGGCGACTACGTGGgtaagttgcggatttatgta-tttgctcagatgcccaattttaatttcttcttcctttaaagtgtctgtgacccaatgcgagtggcacttgtggtgaaaga

upper sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ22002 (Selaginella moellendorffii), 5'ss of exon 1
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt
||||||||||| |||||||||||| ||||||| || |||||||| ||||| ||||| || || |||||||| ||||| ||||| |||||||| ||||| ||| ||||     |        ||     |  ||     |   ||| |   | ||                                              
TGCGGCGACATCCACGGCCAGTTCCACGATCTGATTGAGCTCTTCCGGATTGGAGGCAAGGCCCCCGATACGAATTATCTCTTCATGGGCGACTATGTCGgtgagttctagataggaagaattggtcgttgctacgagttgatctatggttttccag-------------------------------------------

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|9565776|gb|BE475285.1|BE475285
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|193679637|gb|FK621107.1|FK621107
EST:     AGGAGGAAACGCTCCCAATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|207820805|gb|GD792572.1|GD792572
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|11274240|gb|BF324608.1|BF324608
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|213594105|gb|DB961965.1|DB961965
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|207773388|gb|GD744484.1|GD744484
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGG
EST: gi|209728097|gb|BW655332.1|BW655332
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|6951735|gb|AW423803.1|AW423803
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|213599087|gb|DB966389.1|DB966389
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTG
EST: gi|6134267|gb|AW132660.1|AW132660
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|17518767|gb|BM187809.1|BM187809
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|7926631|gb|AW832657.1|AW832657
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTGTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
EST: gi|209721240|gb|BW659228.1|BW659228
EST:     AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAG                         ATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG
genomic: AGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttct ... atttatgcagATCGTGGGTACTATTCAGTGGAGACTGTCACGCTTTTGGTGGCCTTGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGCGACATTCACGGCCAGTTCTACGATCTCATCGAGCTCTTTCGGATAGGAGGAAACGCTCCCGATACTAATTACCTCTTTATGGGCGATTATGTAGgttagtttcttcttcttcttcttctctctctctctctctccctctctctctctctctctatatatatatattccattttcttttgtttaattaattagtt

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA