Sequence
atgc intronic sequence ATGC exonic sequence...agggtttatttcctgcgtttatctatgttttctctagtgaaaagtttcaaattttgttgtttcatttactttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
Basic information
species | Glycine max |
transcript | GLYMA16G32360.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G32360.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G51970.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------agggtttatttcctgcgtttatctatgttttctctagtgaaaagtttcaaattt-tgttgtttcatttactttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
||| || | | || || | | |||| | | |||| || ||| | | |||| |||| ||||| | ||| | || ||||| || ||||| ||||| ||||| |||||||||||||| |||||||| ||| | || || ||| |
gtacttatgatataatcagagagatatttggttttttctttgatttggtatggctcttgacattggtttttgatgggtgtgaatgttgcaaaacaaagACCATGAGATGTGCGGATTTTGTGGTGAAAGAGCCGATGGTGATTGGACATGAATGTGCTGGGATCATTGAAGAAGTAGGTGAAGAAGTGAAACATTTAG-------------------------
upper sequence: GLYMA16G32360.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0100g00300.t01 (Vitis vinifera), 3'ss of exon 2
---------------------agggtttatttcctgcg-------tttatctatgttttctctagtgaaaagtttcaaattttgttgtttcatttactttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
|||| ||||| || |||| ||| | | || | | |||| || || ||||||| | |||| ||||| | ||||| |||||||| || ||||| || || ||||| |||||||||||||| || ||||||||| ||||| ||| | |||
attttctgagcaaccaaacaaagggagtatttaaaataaaggggtcccccctttgttccctccatctattgacctctagtcttgtgattg---gtattttcagAAATTGAGATGTGCAGATTTTATTGTTAAAGAGCCTATGGTGATCGGCCATGAATGTGCTGGGATCATTGATGAAGTTGGTCCCCAGGTGAAGTCTCTGG-------------------------
upper sequence: GLYMA16G32360.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
---------agggtttatt---tcctgcgttta-----tctatgttttctctagtgaaaagtttcaaattttgttgtttcatttact--------ttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
| |||||| | || | || | || | | | | | || | ||| | | || | ||| || |||| | |||||||| || ||||| ||||||||||| ||||| |||||||| | ||| || |||||||| | || |||| | | |
tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaaattttgttgtttcatttactttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
tgctcac putative branch site (score: 2)
ctcacttt CT-rich tract
tttcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggtttatttcctgcgtttatctatgttttctctagtgaaaagtttcaaattttgttgtttcatttactttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA
- - - - -ttcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgct