Sequence
atgc intronic sequence ATGC exonic sequence...ctagttatacataggtctggggtcctctctatgtatgcatacttatttgttgcttctggtgtctttgattatcttatgtgttcattctcaaatttgcagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
Basic information
species | Glycine max |
transcript | GLYMA18G04730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 4
ctagttatacataggtctggggtcctctctatgt-atgc--atacttatttgttgcttctggtgtctttgattatcttatgtgttcattctcaaatttgcagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
| | | | | || | | | | | || |||| ||| | | || ||| | | || ||| | || |||| | || |||||| ||||||||||||| |||||||| ||||| || || |||||||| | ||||| ||||| || |||||||||||||| ||| | |||| || ||||
attttgtctcctctatatgctgccttttacacgtcatgctgatattaagttattgtgaatataatattgtattggcacat-tgttttgtgccatgga-acagCCAAGGGTGGAAGCTGCTATGGTTAACGCCAGGATTCGGAAGACTGTTAAAGCAACACAAGCAAAGGTTGGGTACATTGGTCCTCCAGCTGACTTTAACT-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 4
ctagttatacataggtctggggtcctctctatgtatgcatacttatttgttgcttc-tggtgtctttgattatcttatg---tgttcattctcaaatttg---cagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
||| | | | | | | || || || | || | || | ||| | | || | | ||| |||| || | | || |||||| ||||||||||||| |||||||||||||| || || |||||||| | ||||| ||||| || || || |||||||| ||| | |||| |||||||
---gtttcctccatatactgccttttagtcacgtg---atgctgttatgaagttttattgtgaatataatattataatggcacgttctttttgtgctgtggaacagCCAAGGGTGGAAGCTGCTATGGTTAATGCCAGGATTCGGAAGACTGTTAAAGCAACACAAGCAAAGGTGGGCTACATTGGTCCTCCAGCTGACTTCAACT-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 4
--ctagttatacataggtctggggtcctctctatgtatgcatacttatttgttgcttctggtgtctttgattatcttatgtgttcattctcaaatttgcagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
|| || | | | | | | ||| | | | || | | | || || | || | |||| |||| || ||||||| ||||||||||| ||||||| |||||| |||| || || || || ||||| || ||||| || || |||||||||||||| |||||||||||||
ttctgtggatgggatgatgggatgatgggtttctgtggtttgagtaacttataagtatgatttatgttacttgttctaatttgtcataatcaa-ttggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAAGCAACTCATGCCAAGGTGGGTTACATTGGGCCTGCAACTGATTTCAACT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttgcttctggtgtctttgattatcttatgtgttcattctcaaatttgcagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
ctttgat putative branch site (score: 5)
tttgattatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagttatacataggtctggggtcctctctatgtatgcatacttatttgttgcttctggtgtctttgattatcttatgtgttcattctcaaatttgcagcCACGGGTGGAAGCTGCCATGGTTAATGCCAGAATACGCAAGACTGTCAGAGCAAACCAAGCCAAAGTTGGGTACATTGGGCCTGCTACTGATTTCAACTA
- - - - - - - - - - - tcctctc
- - - - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtc