Sequence
atgc intronic sequence ATGC exonic sequence...aaaggaaatattactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
Basic information
species | Glycine max |
transcript | GLYMA14G23710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------aaaggaaatattactggcttttactcaagtgctttttcttt---tttgatttttgcgtttcctttattatt----tattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
| | | | || | | | || | | | || | | | || | | ||| | | | || | || || | | || |||||||| || |||||||||||||| || || || |||||||| |||||||| || || |||||| | ||||||||||||||||| | || |
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 7
---------------------------------aaaggaaatat-------tactggcttttactcaagtgctttttcttttttgattt--ttgcgtttcctttattattt----attctgtgatttataa--tttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
| | || ||| | || || || ||| ||| | | | | || | | | | | | | | | |||| ||| |||| |||||| | || |||||||| || ||||| |||||||| || || ||||||||||| |||||||| || || |||||| |||||||| || |||||||| | || ||
gtaagattatgtatgcctcatttctgttgtttgatggcaattatcttgaaatcctatgttcccatcgcatgcatttaatacgataaatatgttatgacttcctcactgtgtttgcagtctgacattgataaggtttatgcaatttcagGGCTCCAATAGGGCAAGGTTATGGTCTGACTGAAACTTGTGCTGGAGGGACATTTTCAGAGTATGATGACACATCTGTCGGTCGTGTTGGTGCTCCACTA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 7
aaaggaaatattactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
| || ||| | | | |||| | | | || | | | |||| | || |||| |||| || | | || || | || |||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| || |||| || ||||| |||||||||||||| | || |||
-gtaaacgaatccctgaatatctccttgaggcttgctactctccaatatat-cttttcgtccctttccatttctatgatctaacactgatattcct-cagGGCTCCAATCGGTCAGGGATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTT
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
---aaaggaaata-ttactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
||||||| | ||| | | | | | | | || || | || | || || | | || | | | | | | | | ||||||||||| | |||||| ||||| || ||||||| |||||||||||| ||||| || || |||||||||||||||||| |||||||| | || |||
atttaaggaaacacttagctggcaatgtcctacaatcatgcagtatgcaatattatccttcctcttgttgtaattgctctaa---gtgaactgtcatttt-cagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTT
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S15_17V6.1 (Physcomitrella patens), 3'ss of exon 6
---aaaggaaatattactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtga---tttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
| | | | | | || | |||| || || | | || | | | | ||| | || | | |||| || || ||| ||||||||||||| |||||| | ||||||||||||||||||||||||||| | || |||||| || ||| | |||| || || ||
tccacggcatgtgtcagtgtgtacaactcgg-----ttcactcggtctgatgccacgatgctctggtaccttaacttaagaaactgcgtgggttattttcg-gcagAGCTACAATCGGTCAAGGCTATGGTTTAACAGAGACTTGTGCTGGTGGGACATTCACCGAATGGGATGATCGCTCCGTTCGTCGTGCGGGGCCTCCGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttgcgtttcctttattatttattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
ttttgat putative branch site (score: 4)
tttcctttattattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaggaaatattactggcttttactcaagtgctttttcttttttgatttttgcgtttcctttattatttattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
aaaggaaa
- - - - - - -ctggctt
- - - - - - - - - - - - -caagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtg