Sequence
atgc intronic sequence ATGC exonic sequence...taggataatttactgcttttgaattatgaactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
Basic information
species | Glycine max |
transcript | GLYMA16G32820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G32820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g03590.2 (Oryza sativa), 3'ss of exon 5
----------taggataatttactgcttttgaattatgaactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
||| |||||| || ||||| | | | | | | |||| ||| || | | | | |||| | ||| || ||||||| |||||||||||| |||||||||| ||||| || |||| || || |||||||||||||| | ||| | ||||| ||||| || || ||| | |
gtttcttccctagtgtaattt--tgtttttgtagctaaatcagtacattttgttctgattga-actcactctctaacatgtaatttctt-------tgtttttattcaagGTGGAGCCAATTCGTAACTTATTTGCAGCACTCTTCCTTGCAAGCATCGGCATGCTCATACATGTCAAGTTCTTGTGGAATCATGTTGACATATTGCTTG
upper sequence: GLYMA16G32820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G040158_T03 (Zea mays), 3'ss of exon 15
taggataatttactgcttttgaattatgaactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgt----agGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
|| ||| || | | || | | | | ||| || | | || ||| | ||| | |||| || | | || || | |||| ||| | ||||| || ||||||||||| ||||| || |||| |||||||||||||||||||| | ||| | ||||| ||||| || || || | |
--tattactttgcttgatctcggtt-tagcttctttagcatgctttaag-gacatttcatttagtaaagctgcactctctaacgacttttctttttattttaagGTTGAAGCCATTCGCAATCTATTTGCAGCACTCTTCCTTGCAAGCATTGGAATGCTCATACATGTTAAGTTCTTGTGGAATCATGTTGACATATTACTTG
upper sequence: GLYMA16G32820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G51710.1 (Arabidopsis thaliana), 3'ss of exon 15
taggataatttactgcttttgaattatgaac---tatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgt--tgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
|| || || | || | | | | || | | | || || |||| || || || || | | ||||| |||||||||||||||||||||| || ||||| ||||||||||| || ||||| || |||||||| |||| ||||| || |||||||| |||||||| | | |
---------gtattgattctaaactcaggtcgcttttgctttgcgagtacgtggt-acaaaatgaagtcttaaggtggtggaatctcccttactttgtgatgtagGTGGAACCAATTCGTAATCTGTTTGCCGCTCTCTTTCTATCTAGTATCGGGATGCTCATTAATGTTCACTTTCTATGGAACCACGTGGATATCCTTCTAG
upper sequence: GLYMA16G32820.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv16s0022g02060.t01 (Vitis vinifera), 3'ss of exon 15
----taggataatttactgcttttgaattatg-aactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
| | || | || | ||||| | || | | | ||||||| |||||| |||| | || | | | | | | |||| ||||| ||||| || || |||||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||| |||| |||||||||||| ||| | |
gttccctctttactt-caactgtagaattctccaagtttttatcatgtttcttttgtcataagaatgaa----ttttctgtatctgtcgcttttctatgttctagGTTGAACCGATCCGGAACCTATTTGCAGCTCTCTTCCTTTCAAGTATTGGAATGCTCATACACGTGCAGTTCCTATGGACCCATGTGGATATATTGCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
aagattaaagaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggataatttactgcttttgaattatgaactatgaactatgtttcagttgtcacaagattaaagaaaaacgttctcttaaaagtgcatatttgttgtagGTGGAACCAATTCGTAACCTATTTGCAGCTCTCTTTCTCTCAAGTATTGGAATGCTCATACATGTGCACTTCCTTTGGAACCATGTGGATATTTTGTTGG
- - - - - tactgct
- - - - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - -tgtcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgcat