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

TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact...

Basic information

species Glycine max
transcript GLYMA04G08530.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 5'ss of exon 2
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatg-acctatgtc-tggaact--
|||| | ||| ||||| |||||||| | ||||||||||||||| || ||||||| |||||||||||| |||||||| ||||| || ||||| |||||||||||||         |||  | ||  || | || | || |      |      | |   || |  |  |   ||||  |   | |     | ||  | | | |  
TCAAGGTGCGGCCCGAGGCCGGCGACTACACCATCTTCATGGGTCTCGACAAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttc---ccgcccgccgccttttctcttctgctacgctagcttgattgattgattgattgcc-cgaggattggtaggaggtggtcacgtggtagtattga

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G157332_T07 (Zea mays), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgc-------aaactctctgctcccgacacagattattcacatg-acctatgtctggaact
|||| ||||| ||||| |||||||| |  |||||||||||||| ||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||||||  | | ||||| |   |   |   |  | |||  | ||| ||         |||   | || || |        ||  |    || |    ||||       
TCAAGGCGCGGCCCGAGGCCGGCGACTATACCATCTTCATGGGTCTTGACAAGTACGAGAACGAGGACCTCATCAAATACGGCTTCCCCGAGGACATCTGgtaacctca-tcttcccttggtcgtgtgggtgctccttagtggttaccagtcgcgtgaaatcgtttgttctctgtgttttttgctggtctgtatacttgtc-------

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcaca---tgacctatgtctggaact-
|||| || || || || || ||||| | ||||||||||||||| ||||| |||| |||||||||||| |||||||| ||||| || || |||||  |||||||| ||     |    |||   ||| || |   | ||   || |     |   | | || | |       || | ||| |     |   |  || | ||| | 
TCAAGGCCCGTCCTGATGCTGGCGACTACACCATCTTCATGGGGCTTGATAAGTTCGAGAACGAGGAGCTCATCAAGTACGGCTTCCCTGAAGATGTCTGgtaagccg----tcttaatcgagaatcttctcgatttttcccgatcatctattgtttttgtttcgtttctcgagttttctcggatcggtatcagttttgaattg

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgta-accctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact-
||||||| || || || || |  |||| |||||| |||||||| || || ||| |||||||||| ||  | |||||||| ||||| |||||||||||||||||  |  |  | || || | ||   |  |  ||  ||| |   |||          | |      ||    | || |     ||   |  |    |||   
TCAAAGCCCGACCAGAGGCTGCTGATTACACCATTTTCATGGGTCTCGATAAGCACGAGAACGAAGAGTTGATCAAATATGGTTTCCCCGAAGACATCTGgtacgctttgctgtttccttttcttttggtgcttcacttttgatttttttttttaaatttataattgaggttggtt-tctgtttggt-tgcggagagaatcg

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S24_116V6.1 (Physcomitrella patens), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact----
|||| || || |||||   ||| || |    ||| | |||||||||||||||| ||||||||||||| || ||||| || || || || || || ||||||| |   |  ||||  | | |   || ||   ||||||   ||||  || |   |  ||| ||  |     | |     |  |  | |   | | |   |    
TCAAGGCCCGTCCCGAGTGCGGGGACTATGTCATATACATGGGCCTTGACAAGCACGAGAACGAGGACCTTATCAAGTATGGCTTACCGGAGGATATCTGgtgagtgtt-ttttgtctttttgtatgttgagtttcttgg-cgttgacg-atgattgctgttcgtggtgttg-tggacgatgtttcgtgaatttagggtttggc

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact
|||| ||  | ||||| |  ||||| |||||||||| |||||| || |||||| ||||||||||||| |||||||| || || || ||||| || ||||||||   | |||| | |  |  || |    ||||| ||  || |  ||  |  |                                               
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag----------------------------------------------

upper sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ26605 (Selaginella moellendorffii), 5'ss of exon 1
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact
|||| ||  | ||||| |  ||||| |||||||||| |||||| || |||||| ||||||||||||| |||||||| ||||| || ||||| || ||||||||   | |||| | |  |  || |    ||||| ||  || |  ||  |  |                                               
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag----------------------------------------------

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|151406482|gb|EV276297.1|EV276297
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|213597525|gb|DB964430.1|DB964430
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298178450|gb|HO024185.1|HO024185
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298170636|gb|HO019260.1|HO019260
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|151394888|gb|EV264759.1|EV264759
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298178024|gb|HO023873.1|HO023873
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|14011293|gb|BG726224.1|BG726224
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|192327625|gb|FK020658.1|FK020658
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298185114|gb|HO030327.1|HO030327
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|17518633|gb|BM187675.1|BM187675
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298182837|gb|HO031572.1|HO031572
EST:     AAGTACGATAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGCCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|192303639|gb|FG994533.1|FG994533
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTGTGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|151412807|gb|EV282619.1|EV282619
EST:     AAGTACGAGAACGAGGAACTCATCAAATGCGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|192299132|gb|FG992878.1|FG992878
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|298191108|gb|HO038587.1|HO038587
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
EST: gi|8282557|gb|BE020118.1|BE020118
EST:     AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTG                         GTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA
genomic: AAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaa ... tccattgtagGTTCCATGTCGATAAAATGTCTTCAGCCCATGTCTATGTCAGGTTGCACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctgc