Sequence
atgc intronic sequence ATGC exonic sequence...catttaacataaaattcaacaaattgtcacacaatctcatttttttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
Basic information
species | Glycine max |
transcript | GLYMA13G00580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G099452_T01 (Zea mays), 3'ss of exon 6
-catttaacataaaattcaacaaattgtcacacaatctcatttttttacttct---ggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
| | || | || || ||| | || ||||||| | || | | || | || | | |||| | | || | | | |||||||| | ||||| || || || |||| |||||| ||||||||||| || || ||| ||||||| | |||||| |||||||| |||||||| ||| |||
ctaaacagtggaacaaacatgaagttga-atgtaacttcattttctagtttttttaagcatccaatgtgtgggaatataatccatgga---tgcctatttgcagGCTGTTCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGACCCAATAGCCCACCAACAGCTACAAGGACTACTTTTTTGAATCCTTTTGACGCTGCAC
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------------catttaacataaaat--tcaacaaattgtcacacaatctcatttttttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtcta------------cagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
|||| || | ||| || | | |||| | | | || | ||| ||| | ||| || ||| | | || |||||||| |||||||||| ||||| | || || || ||||| || |||||||||||||| |||| ||||| || || ||||| || |||||||||||||
gtaagcaagaacttagcacactactaaattgttccaaatatatgaaataatgtcttctcctgctgaatttgttctagtttcttcatagctctgcttctttgttctgttttgagaatcttcacataatctcttaaactgactacttccatgaatctaaacatgtatgcttttctgagcagGCTGTTCATGATGGAGTAGATATTTTGAGTCTCTCGGTTGGTCCAAACAGTCCTCCAGCTACTACAAAGACAACATTCTTGAATCCATTTGATGCTACAC
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 6
-----catttaacataaaattcaacaaattgtcacacaatctcattttt-ttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
|| || || | |||||| | |||| ||||| || | ||||| | | | | || || | | | |||| || ||||||||| |||||||||| ||||| || ||||| |||||||| || || |||||||| || |||||||||| ||||| ||||| || ||||||||||| |
ccggttatctattttagatttcaacga---gtcaagtaatcttataactgctactttccatggagattatctatgttgatattaaaagagattttcatg---acagGCTGTTCATGATGGAGTTGATATCCTGAGCCTCTCAGTTGGTCCAAATAGTCCTCCCACAACTACCAAGACAACGTTCTTGAATCCATTTGATGCTACCC
upper sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 6
catttaacataaaattcaacaaattgtcacacaatctc-atttttttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
||| | |||| | || || | | || || || || | | || || | | | ||| | | || | | || ||| ||||||||| ||||||| ||||| || |||| || || || || || || |||||||||||| | |||||||| |||||||| ||||||||||||||| |||
-ttttgcccatgaattaagcatctttttaggtgatatctgttggggtattctttgttttttgttttttcgtttattaattgaagacttcttctgtgaacagGCTGTTCATGATGGTGTGGACATTCTCAATCTCTCTGTGGGGCCAAATAGTCCTCCAGCAACCACCAAGACCACGTTTTTAAACCCTTTTGATGCTGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
ttctaat putative branch site (score: 2)
tattctatctaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttaacataaaattcaacaaattgtcacacaatctcatttttttacttctggtattctatctaaaattttctaatttacaaaatttgggtgtctacagGCTGTGTATGATGGAGTGGATATACTCAGCCTTTCAGTTGGACCCAACAGTCCTCCAGCAGCTACCAAGACTACGTTTTTGAACCCTTTTGATGCTACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - -cacacaa