Sequence
atgc intronic sequence ATGC exonic sequence...tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
Basic information
| species | Glycine max |
| transcript | GLYMA18G43160.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 1
-------tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatt-tccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| || ||| |||| | | || | | | | || ||| | ||| | | || ||| || || | | ||| ||| | ||||||| | || || |||||||| |||||||||||||| |||||||| |||||||| ||| | || |||||||| |||||||| ||||||||||| || ||
ttttgtaagacacctcttcacatttccctgtgaaatgcctgtatgctatat-attta-aatatataaaatgttta--atctgatcc----actatcttgattgttcagGTGAAAAATTTTCTGAAATTGTGGGAAGTCCATATTACATGGCTCCTGAAGTGCTGAAGAGAAACTATGGACCTGAAATAGACATATGGAGTGCTGGTGT
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
tgctgtctactcatgtttcgacatta-tatttcaatctttttcat-tgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| || || || ||| | | || | || || | | | ||| | || |||| || || | || || |||||||| ||| || |||||||| ||||| |||||||| ||||||||||| || | ||| | || ||||| || ||||||||||| ||||||||||||||
--tggactcacagtgcttgtacaacagttgatcgttgttctttgtatacagacaaaactcctagttccatccagtccttatgtgattgttatgttcttttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 1
tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatg----tgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | || ||| | |||| | || | || || || ||| || | | | | | | |||| |||||| | ||| || |||||||| ||||||||||| || |||||||| ||||| | ||| |||| |||||||| |||||||| |||||||| || || ||
----gcaaaggcttgcctcggttcccttcttcagaccccactcatgtggccgtcttcccactttatttatttgaaactcataaaagcattgttttcttttctagGTGAAAAGTTTTCGGAAATTGTGGGAAGTCCATACTACATGGCTCCTGAAGTCTTGAAGAGGAACTATGGACCTGAAATAGACATATGGAGCGCTGGTGT
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
tgctgtctactcatg-tttcgaca-ttatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | || || | | | || | || | | | | | | | | | |||| || || | | | | |||||| | ||| ||||||||||| ||||| || ||||| |||||||| ||||| | ||| | || ||||| ||||||||||| ||||||||||| |||||
--tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
tgctgtct-actcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaata--taaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
||| | | ||||||| ||| | || | ||| | || | | | | | | | ||| | | ||||| || | || |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||
-attgtaggatttatgtttcttgattg--atacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
upper sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttaca-gtatctgacattttttccatgtgttgtgggtaatataaa------aatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
|| | | || ||||| ||| ||| | | || | | | | |||| | | | | |||| || ||| ||||||||||||||| ||||||||||||||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||
-------tagttgcaaggctttatcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctgtctactcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
tgctgtc
- - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - gtatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg
