Sequence
atgc intronic sequence ATGC exonic sequencegtatgttctaatgctctatcctgaactccatttattcccctcaaattattcatgcactaaatgatgaattgatctttgattttgaaagcattattctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
Basic information
species | Glycine max |
transcript | GLYMA17G11600.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 4
-----------------gtatgttc-taatgctctatcctgaactccatttattcccctcaaattattcatgcactaaatgatgaattg-atctttgattttgaaagcatta--ttctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
||| | | | || || | ||| | || || | || || | | | || |||| ||| | || | ||||| | || | |||| | | | | |||||| || ||| | |||||||||||||||||||| ||| ||||||| || || |||||||| ||||||||||| ||||| || | ||| || |||||
gcatgtgctaaatttatctatttccattattacctgtactgctgtgcacataacagtgtaaaccaatggcttagccatatctccaattatatcagtacacttcagagcatgagatttacttctttactacaatgctgcccctagGTTGTACCCCTTTACATTGGGCTGCTATTAGGGGGAACCTGGAGGCATGCACTGTGCTAGTTCAGGCTGGCAAAAAGGATGACTTGATGGTGAAGGATAA
upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 4
-----------gtatgttctaatgctctatcctgaactcca--tttattcccctca----aattattcatgcactaaatgatgaattgatctttgattttgaaagcattatt------ctagtttttattttc--ctta------ttcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
|| ||| | | |||| ||| | | ||||| | ||| ||| | | || || | || ||| | || || || | | | || |||| | || | || | ||||||||||||| | |||||||||||||| | || || |||||| | || || ||||| || |||||||| || ||||| ||||||||| || || ||
gcacgtgtttagttagtttttctagctcttcctaaaccctatctttatactgatcatgacaatctaacctacaacaagcatttaagcacgcttcccctgcattagttttgttggatatcaaatattcatttccagctcaaatgcttttcattagGTTGCACTCCTTTGCATTGGGCTGCTATCCGCGGGAATTTGGAGTCATGCACTGTGCTGGTTCAGGCTGGTAAAAAGGAGGATCTTATGGTGCAAGACAA
upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 4
gtatgttctaatgctctatcctgaactccatttattcccctcaaattattcatgcactaaatgatgaattgatctttgattttgaaagcattattctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
| |||| ||| ||| | | ||||| ||| |||| | | | || | | | ||| |||| || ||| | | | | | || || | |||||| |||||| | || |||||||||||| |||| ||| | ||||| || || |||||||| |||| |||||| ||||| ||| | ||| || || ||
gcatgtgtaaat---ttattccatgcctatattatttat----aataattcct----ttggtaattatatcagctt--atttggatgatatttcttttaactgcgcatgc--tactc--ttagGTTGTACTCCTTTACACTGGGCTGCTATTCGGGGGAACCTTGAGGCATGCACTGTGCTAGTTCAGGTTGGCAAAAAGGATGATTTGATGGTGAAAGACAA
upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttctaatgctctatcctgaactccatttattcccctcaaattattcatgcactaaatgatgaattgatctttgattttgaaagcattattctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
| | | ||| | || | |||| | || | | ||| | | ||| || ||| |||| || |||| | || ||||||||||||||||| ||||||||||| || | || || |||||||| || || || | || |||||||| ||||| || ||| | ||| | |||| ||
-----------------gtggttacaaacatattttttttttaaatcttctttgtttattttcttagattaactatacgtttctaa--catc-ttctccgttatattgattctgtt--atcagGTTGCACTCCTCTGCATTGGGCTGCCATCCGAGGTAATTTGGAGGCTTGCACTGTCTTGGTGCAGGCTGGAAAGAAAGAGGATTTGATGATTACTGACAA
upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttctaatgctctat-cctgaactccatttattcccctc--------aaattattcat-gcactaaatgatgaattgatctttgat---tttgaaagcattat--tctagtttttattttcc--ttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
||||| | | |||||| | ||| || || ||| || || | ||| ||| | | | || | | | || || | | | | | | || || ||| | | || ||| | || | ||||||||| || ||||| |||||||||||||||||||||||||| ||||| || || ||| |||| |||||||| |||||||| || || ||| || | || ||
gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatctttgattttgaaagcattattctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
tttttattttccttat CT-rich tract
attattctagttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttctaatgctctatcctgaactccatttattcccctcaaattattcatgcactaaatgatgaattgatctttgattttgaaagcattattctagtttttattttccttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT