Sequence
atgc intronic sequence ATGC exonic sequencegtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
Basic information
species | Glycine max |
transcript | GLYMA08G01750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------------------------------gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
| |||| | ||||| | | | | ||| ||| || ||| | | | | ||| || ||||| ||||| ||||| ||| | || |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || |||| || |
gtagtattctgctcttatttcccctataataccaccttacatgacttagaccaacaattaacgtggagaaaatttccatgtgcttcactggagtgccgtaattaactctaatggaaaaacaaacaaaa-acattacagtttgttctgacaattttagtttgttccttaattcgaggtacttgtatatggttgcagGGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
| |||| | ||||| | | | | ||| ||| || ||| | | | | | |||| | ||||| || || ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || |||| || |
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaa-tgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatg-gttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 2
-----------gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
| | || | | | | || | | |||| | || | || ||| ||| ||| | | |||| |||| || |||| ||||| ||||| ||| | || ||||| || || |||||||||||||| |||||||| ||||| || ||||| ||||||||||| || || | || |
ctttaaatgccacatccaaatagaag-gttatgcagttttttaatgatggct-ctagtttctcagtttatctttgtaacctgaattgtttgtatg-gatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATC
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 2
gtaggctaacatttgcatcaacaagatgtctaatattttcttcc------agattcatttg---ttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
| | | | || ||||| | | | | |||| || | | | || ||| ||||| || |||| || | || |||| ||||| ||||| ||| | || ||||| || || |||||||||||||| |||||||| ||||| || ||||| ||||||||||| || |||| ||| |
ttgagatgctacagccaaacacaagttatgcagttttttttttcttctgatggctggcttcagtttatctttgcaaccttacttgtttctacg-gatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATC
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaat----tgcatgttttgtt--gtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
||| | | || ||| | || || ||| || ||| | ||| || | | || | ||| ||| || ||| ||||||| ||||| ||||| ||| | || ||||| |||||||| || |||||||| || |||||||| || |||||||| |||||||||||||| |||| || |
gttaacattctcctgtgtttcatcttttgagccgtttattatttatatacattttcagcctgtagaacatgttagcttcatatacaacacaatgatcggtatattataaggtttcagtcttttttttttttttgctgtagataactcgttctgtccttttgttgaccagGGAAAGCAAAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATC
upper sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
----gtaggctaacatttgcatcaacaagatgtctaata-----ttttcttccag-attcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
| || | | | | || || | ||||| | | || | |||| ||| | | || | ||| || ||||||||||| ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| ||||||| ||||
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattatt--gttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
attcatttgttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG