Sequence
atgc intronic sequence ATGC exonic sequence...tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
Basic information
species | Glycine max |
transcript | GLYMA20G33140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g65230.1 (Oryza sativa), 3'ss of exon 3
tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
| | | || | | | ||| | | || || | || || || | || | | | ||| | ||||||||||||| || || ||||||||||| || || ||||| |||||| |||||||| ||| || || | |||| ||| || | || ||||| ||| |||
----------gttggtgtcgt-gctgctcacaatgccaacaatgcggataatttatcttgtat---atttgcttcttatgcatggggttt-tgcttgcagAAAGGTCGCCTGTCTGAGGATGAGGCCCGGTTTTATGCTGCTGAAATTGTTGATATTCTGGAGTATTTGCATAGTTTAGGCCTAATTCATCGGGATGTTA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G097821_T02 (Zea mays), 3'ss of exon 3
tttttggaatatggaagctgttaatttgtaag---ctagtaactttctgcatg-cttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
|||| | ||| || | || || | | || | || ||| | | | || | ||| ||||||||||||| || || ||||| || ||||| |||||||| |||||| |||||||| | || ||| | ||| | || | || ||||| ||| | |
-------------------gttagtgtgttagtgtccagctgctaacagtgtgattcatttctgtcctgcctttgtttcttgtgcttataattc--ggttgcagAAAGGTCGGCTCTCTGAGGACGATGCACGGTTCTATGCTGCTGAAATTGTTGATATATTGGAGTACTTGCATGGCCTTGGCCTAATTCATCGGGATGTCA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 3
tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtg-cagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
| ||| | ||| || || |||| | || | ||| | || || | | | || || ||| | | || ||||||||||||||||| |||||||| || || ||||| || ||||||||||||||||| || || ||||||||| ||||| | |||||||| |||||||
------------gtaagatattatttgagaatctaggagattgattcatattct------caaaatgtagttgcgttatggttttgttttgtgtttggcagAAAGGTCGTCTATCTGAGGATGAAGCTCGGTTCTACAGTGCAGAAGTTGTTGATGCTCTTGAGTATATACATAATATGGGACTGATACATCGAGATATTA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 3
tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
|| | | | | | | | | | | | | ||| |||| ||| || | | || | || | ||| | ||||||||||||||| ||||| |||||||| || || ||||| | || |||||||| |||||||| || || ||||||| | ||||| | || ||||| |||||||
--------gtaagatgatcgctgaatcttgggagattgattcattcaatg-ttgtcggaatttgacat--aacatcatggttcc---tttttttgtgcagAAAGGTCGGCTATCGGAGGATGAAGCTCGGTTCTACACTGCAGAAGTTGTGGATGCTCTTGAGTATATACATAGTATGGGACTGATTCATCGAGATATTA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 4
tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagattt--ctgatttctatg--tgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
|| ||| || | || ||| | | || | | | ||||| | |||||| | | ||| | | || || |||| | || |||||||||||||| | |||||| |||| || || |||||||||||||||||||| |||||||| ||||| || |||| | | ||| | ||||| || |||||||
ttcttg--atcttaaatttgtctctgcttcttgta-tgtggtgcatcatgcctacaactgcaagtttgctatt-gtaacatccagtgaatttgtgtgagtgcagAAAGGTCGTTTGTCAGAGAATGAAGCTCGCTTCTATGCAGCTGAAGTTGTAGATGCTCTTGAATATATTCATAGTCTAGGATTGATACACCGGGATATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
ttctgat putative branch site (score: 3)
tttctat CT-rich tract
atttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttggaatatggaagctgttaatttgtaagctagtaactttctgcatgcttgttactgcatgatatctactagcaagatttctgatttctatgtgcagAAAGGTCGTCTATCAGAGGATGAGGCACGATTCTATGCAGCTGAAGTTGTTGATGCTCTCGAATACATACATAATTTGGGAGTCATACATCGTGATATTA
- - - - - - -gaagctg
- - - - - - - - - - - - - tgtaagc
- - - - - - - - - - - - - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat