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

TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgagtggaaaattatatccttgtgtttttattatttatggtttaccttgcagttaaagtccatccaacccctcataattgttggagtaccaatt...

Basic information

species Glycine max
transcript GLYMA10G36280.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 10
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgt-tgagtggaaaattatatccttgtgtttttat--tatttatggtttaccttgcagttaaagtccatccaacccctcataattgttggagtaccaatt
|||||| ||||| ||||||||||| ||||| || || ||||| || || ||||| |||||||| || || || || |||||||| ||| |||| ||||||||| ||   |    |   ||||||  | | |     ||   | || ||||||   ||    ||   || ||| | |    || |    |    |       | 
TTTTGGCTATGGAATCATGCTTCTTGAGCTCATTACAGGACAAAGGGCATTTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtaccaccacatctttatatattggggcaaccatggaagttttggttttgtttttcctt---gtgcatgctagttgtcctccaggacacatctttctta

upper sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 5'ss of exon 10
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgta--tgttgagtggaaaattatatccttgt-gtttttattatttatggtttaccttgcagttaaagtccatc--caacccctcataattgttggagtaccaatt
 ||||||||||| || |||||| ||||||| || || |||||  | || |||||||||||||| || || ||||| |||||||| ||||| || || ||||||  ||   ||   ||  ||  || |   | |   |   |||| |||   |    ||   | |   |   |    |       | ||||  |    |       
ATTTGGTTATGGGATTATGCTTTTGGAGCTTATAACAGGACAACGTGCCTTTGACCTTGCTCGTCTAGCCAATGATGATGATGTCATGCTACTGGACTGGgtaattgactagcacaatcttcaattcaaattgcagtccatattcatgcccttttgtggcttgatgttgtgttgggagttagataaaattacttttatgt-----

upper sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G150024_T01 (Zea mays), 5'ss of exon 10
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgagtggaaaattatatccttgtgtttttattatttatggtttaccttgcagttaaagtccatccaacccctcataattgttggagtaccaatt---------
|||||| ||||| ||||||||||||||||| || ||||||||||| || ||||| || ||||| || || ||||| |||||||||||||| ||||| |||||| ||       ||| ||   ||    |  |  || |      |  |||||   |     |  | |||     |  |||||    ||    |  | ||          
TTTTGGATATGGGATCATGCTTCTGGAGCTTATTACTGGACAGAGGGCATTTGATCTAGCTCGTCTTGCAAATGATGATGATGTTATGCTTCTTGACTGGgtaagt-------aaattttcttctcaatagtcatagtgccacagtattaccgcactacagatatacatttt-tctttcata-ccattttgctgtctatgggctatatt

upper sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G115420_T01 (Zea mays), 5'ss of exon 10
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgagtggaaaattatatccttgtgtttttattatttatggt-ttaccttgcagttaaagtccatccaacccctcataattgttggagt--accaatt----
|||||| ||||| ||||||||||||||||| || ||||| ||||| || ||||| || ||||| || || ||||| || ||||||||||| ||||| |||||| ||       ||| ||   ||    |     | | |   |  || ||||| ||      |      |     |  ||||| || |||  ||  |     |    
TTTTGGCTATGGGATCATGCTTCTGGAGCTTATTACTGGCCAGAGGGCATTTGATCTAGCTCGTCTTGCAAATGATGACGATGTTATGCTTCTTGACTGGgtaagt-------aaattttcttctcaatacaagtgtcacacacagtattaccgtgtgacagattatatttttttctttcatactttttgctgtctatgggctatat

upper sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 5'ss of exon 10
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgt-tgagtggaaaattatatccttg--tgtttttattatttatggtttaccttgcagttaaagtccatccaacccctcataattgttggagtaccaatt
||| || ||||| || |||||||||||||| |||||||| |||||||||||||| |||||||| || || ||||| |||||||| ||| |||||||||||||| |  | | ||     ||  | |||    || ||  |  | |||  |    | ||||   ||   |  |  | | |    |||| ||      | |  |  
TTTCGGGTATGGAATTATGCTTCTGGAGCTAATCACTGGGCAGAGAGCTTTTGATCTTGCTCGGCTTGCCAATGATGATGATGTCATGTTGCTTGATTGGgtaagcattactgtctttttccaccctatactgattagaccacttactgccccctttgccagtattttttaagctaacagg-ataaatgccatctttctta--

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|193426656|gb|FK391279.1|FK391279
EST:     TGCTCGACTCGCTAANGACGATGATGTTATGCTGCTTGATTGG                         GTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT
genomic: TGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgag ... attttcacagGTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT
EST: gi|207833525|gb|GD806770.1|GD806770
EST:     TTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGG                         GTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGAT
genomic: TTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgag ... attttcacagGTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGAT
EST: gi|5606012|gb|AI900110.1|AI900110
EST:     TTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGG                         GTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT
genomic: TTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgag ... attttcacagGTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT
EST: gi|193422890|gb|FK389257.1|FK389257
EST:     TGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGG                         GTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT
genomic: TGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgag ... attttcacagGTAAAAGGACTTCTGAAAGAGAAAAAGCTTGAAATGTTGGTAGATCCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGGTTATGGTATCATGCTTCTGGAGCTGATCACTGGACAGAGAGCTTTTGACCTTGCTCGACTCGCTAATGACGATGATGTTATGCTGCTTGATTGGgtatgttgagtggaaaattatatccttgtgtttttattatttatggtttaccttgcagttaaagtccatccaacccctcataattgttggagtaccaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacccc