Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

Basic information

species Glycine max
transcript GLYMA07G18310.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 1
---ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatt-tccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | |||| | || | | || | || || | | | ||| | |||| || | | ||| ||| | ||||||| | || || |||||||| |||||||||||||| |||||||| |||||||| ||| | || |||||||| |||||||| ||||||||||| || ||
ttttgtaagacacctcttcacatttccctgtgaaatgcctgtatgctatatatttaaatatataaaatgtttaatctgatcc----actatcttgattgttcagGTGAAAAATTTTCTGAAATTGTGGGAAGTCCATATTACATGGCTCCTGAAGTGCTGAAGAGAAACTATGGACCTGAAATAGACATATGGAGTGCTGGTGT

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacag-tatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | || | | | | || | || ||| ||| ||||| | | || || | | || || | || || |||||||| ||| || |||||||| ||||| |||||||| |||||||| || || | ||| | || ||||| || ||||||||||| ||||||||||||||
-tggactcacagtgcttgtacaacagttgatcgttgttctttgtatacagacaaaactcctagttccatccagtccttatgtgattgttatgttcttttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | | | | || | | |||| | | ||||| || | | | | | | |||| |||||| | ||| || |||||||| ||||||||||| || |||||||| ||||| | ||| |||| |||||||| |||||||| |||||||| || || ||
gcaaaggcttgcctcggttcccttcttcagaccccactcatgtggccgtcttcccactttatttatttgaaactcataaaagcattgttttcttttctagGTGAAAAGTTTTCGGAAATTGTGGGAAGTCCATACTACATGGCTCCTGAAGTCTTGAAGAGGAACTATGGACCTGAAATAGACATATGGAGCGCTGGTGT

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
---ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | | | | | || | || | | | | | | | |||| | |||| | | || | | | | | |||||| | ||| ||||||||||| ||||| || ||||| |||||||| ||||| | ||| | || ||||| ||||||||||| ||||||||||| |||||
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacaca-agtaaacccta-gttttatctggccttttctca-tcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
--ctcatgtttcac-tttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | || | |||| ||| | || | ||| | || | | | | | | | || ||| || || || | || |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||
attgtaggatttatgtttcttgattg--atacatacctttgatgtattttgaccagtttatttggtgttgatgctgt-ttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttaca-gtatctgacatattttcc--ataatgtgttgtgggtaa-tataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
|| |||| || ||||| ||| ||| | | || | | | | || | | ||| | | | || ||| | || ||| ||||||||||||||| ||||||||||||||||| ||||| |||||||| || || |||||||||||||||||||||||||||||||||||||||||||||||
tagttgcaaggcttt----atcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

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|16277961|gb|BI942654.1|BI942654
EST:     TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAG                         GTGAGAAGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGGAG
genomic: TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAGgtacgctgaa ... aaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAG
EST: gi|16277967|gb|BI942657.1|BI942657
EST:     TTCGCCGCTCAACGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAG                         GTGAGAGGGTCTTAGAAATTGTT
genomic: TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAGgtacgctgaa ... aaatttccagGTGAGAGGTTCTCAGAAATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
                                                tttcc  CT-rich tract
 taatataaaaatttcc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

-tcatgtt
- - - - -cactttc
- - - - - - - - - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - tctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg