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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG

Basic information

species Glycine max
transcript GLYMA03G38340.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
----ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgc-ttatagaagt-ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG
    ||   ||| |   | |||  || | |  | | |  | |||   |||    || |  |  || |  ||  | |  ||   | || |  || | ||    ||||||| |||||||| ||||||||||||||||| || ||||||||  | || ||||| || || | ||||
cctgtttccatgatggcgaatag-gtggttgacctatgcactagggaata----gggatatattcatcatctctggc-tgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
-ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaac-tttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG
 ||||| |    || | |  ||| || |     |  |     |  |   ||||       ||  |  | | |||||       | |||   ||   || |||||| ||||| ||||| |||||||| ||||| |||||||||||  | || || || ||||||| ||||
tttaatgtatcctttgtttatgt-gcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctctt-cagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10880.1 (Arabidopsis thaliana), 3'ss of exon 2
ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG-----------------------------------------------------------------------------------------------------------------------------
                               || ||  |||     |  ||  || ||||  |||      || | | |    ||     || ||  |||||| |||||||| |||||||||||||| ||||||| ||||||| | || || || || ||||  |||                                                                                                                             
-------------------------------gttaaccagtgggc-taatgttacgttgt--tagatgggagtttagcgaccctaccccatttat--caggagccgtgagttcctttggcaagaaggacacactgattttgctaccaaagaagaggctgatgaggaggtgcttgatgtttgaacatctacagCCGCGTGTATGACTCATGGAGATGACAAAGGTTTAGTATTCCCTCCTAAAGTGGCACCTGTTCAAGTTGTTGTAATCCATGTTCCCATCAAAGGCGCTGC

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
-ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcc--tagtccattgtgtggtgcttatagaagtt-tgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG
 | |  || |  |  ||| ||     || | | |    || |  || ||    ||  ||||    | || ||||| |    | | | | |  |  || ||| |||||||| || ||||||||||| || ||||| |||||||||||| ||||||| || ||||||  ||||
ttcatgatcgactatgattct-ccaattccttatttgttaat--atgttaaaaaatcttgtttagttgttcattg-gcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S7_175V6.1 (Physcomitrella patens), 3'ss of exon 4
ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgt-cctagtccattgtgtggtgcttatagaagtttgatt------gcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG
        ||||||   | | ||   |   |||  | |  |  ||  |     | || ||   || |  |        || ||  ||   || | ||      ||||||||||||| ||| | ||||||||||| || ||||| |||||| |||| |||||||||||||  |||
-------tgttttgttgatttttatctgggtgttgattgttacatccttgcagagttggtatttacttaaaaaaaaattgattcgagtgtttcgcttcactttgcagGAGTCGTGAATTTTTATGGCAAGAAGGTCATACTGCATTTGCTACAAAAGAGGAAGCAGATGTCGAG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15689 (Selaginella moellendorffii), 3'ss of exon 4
ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgct-tatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG---------------------------------
                                                  | | |||   |    | |  | | ||      ||   || | |  || |||||||||||||||||||||||||||||| ||||| |||| |||  | ||||| ||||| ||||  ||                                  
--------------------------------------------------gtagcttctcctcgattctctttctgagatgatacgtaattctcttttcagGAGTCGTGAGTTTCTTTGGCAAGAAGGCCACACCGCTTATGCAACCAAGGAAGAAGCGGATGAGGAAGTGTATGCGGTGCTTGATCTCTATCGAAGAGTG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ38227 (Selaginella moellendorffii), 3'ss of exon 4
ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgct-tatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG---------------------------------
                                                  | | |||   |    | |  | | ||      ||   || | |  || |||||||||||||||||||||||||||||| ||||| |||| |||  | ||| | ||||| ||||  ||                                  
--------------------------------------------------gtagcttctcctcgattctctttctgagatgatacgtaattctcttttcagGAGTCGTGAGTTTCTTTGGCAAGAAGGCCACACCGCTTATGCAACCAAGAAAGAAGCGGATGAGGAAGTGTATGCGGTGCTTGATCTCTATCGAAGAGTG

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|208296954|gb|GE096564.1|GE096564
EST:     TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
EST: gi|193510235|gb|FK470247.1|FK470247
EST:     TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTT
genomic: TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTT
EST: gi|192304983|gb|FG996115.1|FG996115
EST:     TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         -AGTCGTGAGTTTCTTTGGCAAG
genomic: TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAG
EST: gi|208149140|gb|GD945506.1|GD945506
EST:     GGTGTCAATGTTGTCAGATGGGAGTTCGGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: GGTG-CAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
EST: gi|208322193|gb|GE122164.1|GE122164
EST:     AGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: AGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
EST: gi|207774360|gb|GD746254.1|GD746254
EST:     GGTTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: GG-TGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
EST: gi|207841506|gb|GD811458.1|GD811458
EST:     TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
EST: gi|19053180|gb|BM731847.1|BM731847
EST:     TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAG                         GAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA
genomic: TGGTGCAATGTTGTCAGATGGGAGTTCAGCAACCCCACTCCATTCATCAGgtagtgagta ... ttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctggaactttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG
                                           gtttgat  putative branch site (score: 5)
                                   ttatagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - -ggttttg
- - - - - - - - - ctgttgc
- - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - -attctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg