Sequence
atgc intronic sequence ATGC exonic sequence...tttatggcagatgcatgtctctttatgctatgactttattccttttgaagatggtcttgagggatatttttaattctctttgcattgattgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
Basic information
species | Glycine max |
transcript | GLYMA16G09330.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 4
---tttatggcagatgcatgtctcttta-tgctatgactttattccttttgaagatggtcttgagggatattt----ttaattctctttgcattg-attgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
|| || | | | | | | | || || | |||| | || || | | ||| | ||| | ||| | | | || || ||||||||||||||||||| | ||| | |||||| | | || ||| | || || || | |||||| || |||||||| ||||| ||||||||||||||||||||
gtaactaaacataataccttttcttacacttttgcatctataatggatttgtatttgtgtgtgtgtgtgttttgctgtagattaacattgtttcgtaatgggtgaacagGAACTCCTTGCTTCAGAGGACATGGAAGGAGAACTGGTGAGAGGAGAAGAAAGTCTGTTCGTGGTTGCATTGTGAGCCCTGATCTCTCTGTTCTGAACCT
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------tttatggcagat--gcatgtctctttatgctatgact----ttattccttttgaagatggtcttgagggatattt--ttaattctctttgcattga----ttgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
||| | || | | | | || || | | ||| | | | | || ||| ||| || | || | | |||| ||| | |||||| || ||||||||||||||||| ||||| || || ||||||||||||||||| |||||| || |||||||| |||| || ||||| ||| ||||| |
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
-----tttatggcagatgcatgtctctttatgctatgactttattccttttgaagatggtcttgagggat----atttttaattctctttgcatt----gattgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
| | | || || ||| ||| | |||| | || | || | | | | | | | || || | | || | | | |||| || || |||||||||||||| ||||| || || ||||||||||||||||| |||||| |||||||||||||||| ||| ||||||||| ||||| |
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagttgggtctatgagatttattacactttatgcttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------tttatggcagatgcatgtctctttatgctatgactt--tattccttttgaagatggtcttgagggatatttttaattctctttgcattgattgtgtt--aacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
|||| | ||| | | || ||| || || | | | | |||| | || | || || | || || | | ||||||| |||||||| || ||||| || ||||| || |||||| | |||||||| ||| || |||||||||||||||| || || |||||||||||| |
gtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagcatgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttttgcttaagcagGAACCCCTTGCTTTCGAGGATATGGTAGGCGTAATGGAGAGAGGAGGAGGAAGGCTGTACGTGGGTGCATTGTCAGCCAGGACCTTTCTGTTCTGAACTT
upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S31_322V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------tttatggcagatgcatgtctctttatgctatgactttattccttttgaagatggtcttgagggatatttttaattctctttgcattgattgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
| | ||| | ||||| | | | || | | || | | | | || ||| | ||| || || | | |||| |||||||||| |||||||| ||||||||||| ||||| ||| | || | ||| | ||||||||||| || || || ||||| || ||||||||
gtacaatattgattaattggaacctcatggtctgaagttgtgcctgcaaggaatccgtactggatacgcgtctcgtcgtcatgcattcttgtactgcatgtcactaaaatctaatt-tcttaacgattgtacttg-at--gttttctcggcagGTGTCTCTTGCTTCCGAGGATACGGGAGGCGCAACGGCGAGCGTAGGCGAAAGTCCGTTAGAGGGTGCATTGTGAGTCCCGACCTCTCAGTGCTGAACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagatggtcttgagggatatttttaattctctttgcattgattgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
atatttttaattctct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatggcagatgcatgtctctttatgctatgactttattccttttgaagatggtcttgagggatatttttaattctctttgcattgattgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT
- - - - - - gcatgtc
- - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaggga