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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATCGTCGAGCCATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgttcccaaccctaattttgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg...

Basic information

species Glycine max
transcript GLYMA17G17790.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 1
CCAATCGTCG-AGCCATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgttcccaaccctaattttgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg------
 |    |  |  |||||||| | ||| ||||||||| |||| || || || |  |||||||  ||||||||||| |||||| ||||| ||||  ||||||||||| ||      |   || |  |  |  ||     | | ||    ||    ||||   | |      |   |      | || |  |   ||  |          
-CGGCGGCGGCGGCCATGTCGACGGCCCGCGTCTACGCCGACGTGAACGTGCACCGCCCCAGGGAGTACTGGGACTACGAGGCCCTCGCCGTCGAATGGGGgtaagaactgattccttcccacctacgcctc---gccgtgctaccgtgt---gattgtcccccccccccccccccccactcgtgtcgtcgtcgcctagaataacgt

upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 5'ss of exon 1
CCAATCGTCGAGCC-ATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgta-ataatg--ttcccaaccctaattttgtttctggag-ccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg
|| | |||||  || |||||||| || || |||||| |||| ||||| ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||| |||  |  || |    | |||   |  ||| ||||   || | || | ||    || | |  || |      |    ||| || || ||   ||  |   
CCGA-CGTCGCTCCCATGTCCAAAGCTCGAGTCTACGCCGACGTCAACGTTCTTCGCCCCAAAGATTACTGGGATTACGAATCTCTCACCGTTCAGTGGGGgtacatatcgattttctcctcttaaccctaattccggaggtttttttttcttctggtttttgtcttaggttgttgactg-ggatcgtttaatttttgtgat---

upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 1
CCAATCGTCGAGCCATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataa-tgttcccaa-ccctaattt--tgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg
        |    ||||||||  || || |||||| | || |||||  |||  ||||||| ||| |||||||| |||||||| |||||||||||||||||||||| | |  ||  || |||||||||  | ||||     ||  |  || | |    |||   | |   | | | |||| |  || |  || || | | |||  
-------CCAGATCATGTCCAGTGCTCGAGTCTACGCAGACGTCAACATTCACCGCCCCAGAGATTACTGGGACTACGAGTCTCTCACCGTTCAATGGGGgtaatcactactcataaaccctaatttcttctttccttccccacccctttttccactattgatctcgtgttatagtcaacatgtt-tccatgtc-cctgtta--

upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 5'ss of exon 1
CCAATCGTCG--AGCCATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgtt------cccaaccctaattttgtttctggagccttctgttatgctcagattagacaca-gttaacaatcaatagattgtatatttcgcgttt-tagg-----------------------------------------------------------------------------------
    | || |  ||  ||||||||||| || || ||||| ||||| |||||||  || || ||||||||||||||||||||  ||||   ||| ||||||||||||  |   |          |    | |    | ||  | |  ||      | || |   ||  ||||   |  ||    ||  ||        ||| ||   ||                                                                                     
--GGTTGTTGGAAGTGATGTCCAAGGCCCGGGTGTACACGGATGTGAATGTTCAGCGTCCGAAAGAGTACTGGGATTACGAAGCCCTTGTCGTCCAATGGGGgtaaggacactgaatgatttcattgcagtagcatatcgcgtgaatttctccctccttatgatatgcacataattccagctcatgtatgcggatcatcgggtcagtaaaagggactttggtttagtttcagattgtccgtagtatactggtgcttgtgctttccctaacaattgtgtggtttcgtactgcag

upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAATCGTCGAGC--CATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgttcccaaccctaattttgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg---
   |  | |  |    ||||||||||| || || ||||| ||||| ||||| |  || || ||||| || ||||| |||||| |||||||||| ||||||||||||      |  | |  |  |||   |  ||  |  ||||  | || |  |  ||  ||| || || |  |    |   ||   | |   ||  |       
--GACGGCCAGGTGTTATGTCCAAGGCCCGGGTTTACACAGATGTGAATGTCCAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttccatggctattc-gattcactccctttatgcttccttaattccaatgttctacagagatatc--tgggcacggtgaggaatcatcgactagaaacc

upper sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAATCGTCGAGC--CATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgta-ataatgttcccaaccctaattttgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg--
   |  | |  |    ||||||||||| || || ||||| ||||| |||||||  || || ||||| || |||||||||||| | || |||||||||||||||||      ||| | | |        ||  | |      ||| ||| | |  || |     |  | |  |  |   |        | ||||| ||   |    
--GACGGCCAGGTGTTATGTCCAAGGCCCGAGTTTACACGGATGTGAATGTTCAGCGGCCGAAAGATTATTGGGATTACGAGGCTCTTACCGTTCAATGGGGgtatgctccgttactatcttcctcgctgcatttatga--ttccgtt-tccctaggtctcttagggatgtctctacttgacgaagctctttcgtgtaggaattc

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|15663566|gb|BI700937.1|BI700937
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|298197832|gb|HO039371.1|HO039371
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|22522007|gb|BU080818.1|BU080818
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|209714911|gb|BW682076.1|BW682076
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|151399006|gb|EV268877.1|EV268877
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGAACAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|7692114|gb|AW760229.1|AW760229
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|20812535|gb|BQ297013.1|BQ297013
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|6070879|gb|AW100266.1|AW100266
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAAATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|192301709|gb|FG994403.1|FG994403
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGT-GTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|209710355|gb|BW681254.1|BW681254
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|8284576|gb|BE022144.1|BE022144
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|8284215|gb|BE021774.1|BE021774
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|9205122|gb|BE331346.1|BE331346
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
EST: gi|16105199|gb|BI892939.1|BI892939
EST:     CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG
genomic: CTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgt ... tctttttcagTGATCAAGATGATTATGAGGTTGTGCGCAAAGTGGGAAGGGGAAAGTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATCGTCGAGCCATGTCCAAGGCACGCGTCTACACCGATGTCAATGTTCTTCGCCCCAAAGAGTACTGGGATTACGAGTCCCTCACCGTTCAATGGGGgtaataatgttcccaaccctaattttgtttctggagccttctgttatgctcagattagacacagttaacaatcaatagattgtatatttcgcgttttagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaccc