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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgctatgagcacgcattctcgttccccttgtatttggagttttcggggtacatacatgagggtttagagttctgttttctggcctgtg...

Basic information

species Glycine max
transcript GLYMA01G41940.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 5'ss of exon 9
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttc-tgctatgagcacgcattctcgttccccttgta-tttggagttttcggggtacatacatgagggtttagagttctgttttctggcctgtg
 |||||||| || ||||| |||||||| |||||||||||||||||||| ||||| ||||| || |  || |||    |  |||| | | ||||||| |||||| || || |  | |||  |     | |  |  ||    |   | |||  |  ||      | | |   ||      || |      |   |||   |   
AACGGATTCAAGACTCAGGCCAGATCAGCGGCATCTAGAGAATGGGGAGTACGAAAAGGCTAACTCTGAAAAATTGCGCCTGGAGACGAGGCAGAGGATGgtaagtattcttgttctaaaaatttccttaattttttttatcacagtttttaaattcttacctgcttcactgtactcgtacatcgaactacactgaattt--

upper sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G061099_T01 (Zea mays), 5'ss of exon 9
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgctatgagcacgcattctcgttccccttgtatttggagttttcggggtacatacatgagggtttagagttctgttttctggcctgtg
 |||||||| ||||| ||||||||||||||||| || ||||||||||| |||||||||||||||   || ||||   |  | || |  | |||  | |||||    |   | |   ||    |  | || |  ||| | |   |  |  |   |      |       |     | || | |  |        || ||  
GACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGACACAGCAACGGATGgttgtacacattttacattgctatactttttttttctcatgaaagctacatcatgatcactgatcgactccatttctacattgtttgggcactgcttgca

upper sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G409265_T03 (Zea mays), 5'ss of exon 4
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgt-acgtcttttctgctatgagcacgcattctcgttccccttgtatttggagttttcg--gggtacatacatgagggtttagagttctgttttctggcctgtg---------------------------------------------------------------------------------------------
 |||||||| ||||| |||||||||||||| || || ||||||||||| |||||||||||||||   || ||||   |  | || |  |||||| | |||||     |  || |||  ||  | |   || || |     ||  ||   ||    |    |  | ||| | |      || || | |     |    | ||||                                                                                             
AACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGACACGGCAGCGGATGgttgtacccattttgcattg--ctctgcttttcatgaaagttacatcatgatcactgattgactccattcttatattgtttgaatacctgcctggaccttgtggtcttggacgtacgtggtggactgaattccatcgttggatgtctgatgcttttctgccctataactgaagttttgtgtggtcgtcgtctgcag

upper sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgc----tatgagcacgcattctcgttccccttgtatttgg-agttttcggggtacatacatgagggtttagagttctgttttctggcctgtg
||| || || |||||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||||||| |||| ||||   |||| |||||||||||||   | | |     |   |  |        ||   || || ||     |  |||| | | ||||         |  | ||       ||||| |     
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc-----

upper sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 5'ss of exon 8
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgctatgagcacgcattctcgttccccttgtatttggagttttcggggtacat-acatgagggtttag---agttctgttttctggcctgtg
||||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||| |||   || |||| | |||| || ||||||||||| |||||| |  |         |   |     |  ||  |||  || ||||    |  |    | |  || |  | |   ||||    | ||     |||| |      
CACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGAAGCGGCAGAGGATGgtatgagtagctcctcctttccctatttcttcaatccattt-tattcatggcatcattgtttgatgattttattatttaaccaaattggagattcttgtgc---

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|58023109|gb|CX709850.1|CX709850
EST:     GGAAAAGCGGCAGAGAATG                         TCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
genomic: GGAAAAGCGGCAGAGAATGgtacgtcttt ... cattctacagTCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
EST: gi|151393208|gb|EV263083.1|EV263083
EST:     ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATG                         TCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
genomic: ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttt ... cattctacagTCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
EST: gi|192316196|gb|FK011611.1|FK011611
EST:     ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATG                         TCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
genomic: ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttt ... cattctacagTCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
EST: gi|58016065|gb|CX702807.1|CX702807
EST:     CGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATG                         TCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
genomic: CGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttt ... cattctacagTCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
EST: gi|26267946|gb|CA819009.1|CA819009
EST:     ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATG                         TCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA
genomic: ACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttt ... cattctacagTCAAGGAAAATACAAGAAAGTGGTTGGAAGCCTAGATGGTTCCGAAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgctatgagcacgcattctcgttccccttgtatttggagttttcggggtacatacatgagggtttagagttctgttttctggcctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcccct