Sequence
atgc intronic sequence ATGC exonic sequence...tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
Basic information
species | Glycine max |
transcript | GLYMA17G16400.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 2
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggttttttt------gttgagttttgttggtt-ttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| ||| | | || || | | | ||| | ||||| | | | | | | ||| || | || | | | ||||||| || | ||| ||||| | ||||| || |||||| ||| || | ||||||||||| ||||||||||| ||||||||||| || || || || |
-------atttaagtgtgacttgttacaagtagcacttgtttgactgaatggttaatctcacagtgccaaactaagatggaagtttttcttgttgtcttatctgcagGAAATAGCAAGTTACTTGGGCTTAGAACTTGGGAAGATTAACATAAAAAGGTTTGCTGATGGCGAAATATATGTTCAGTTACAAGAAAGCGTAAGGGGAT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 2
--tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtt-tttttgttgagttttgt-tggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| | | | | ||| | | |||| | | | | || | | | | | | || | | |||| | || ||| | | ||| |||| || || | ||| |||| || ||||| || ||||| |||| ||| | ||||||||||||||||||||||| ||||| ||||| ||||| | || |
cctcaatagatttttaatgacgaataattataaacaggaaatatgttatctcgttcatgcctaataatttctttatggtatcct----gtatttttatgaacagGAGATAGCAAGTTACTTGGGGCTAGAACTTGGGAAGATAACCATAAAGAGGTTTGCTGATGGTGAAATATATGTTCAGTTGCAAGAAAGTGTACGGGGCT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| || | | | || | | | ||| || | ||||| || | | | | | | | | ||| |||| ||||||||||| |||| ||||| ||||| || || ||| || ||| ||| ||||||||||||| || || ||||| ||| | |||| |||||||||||||
-----------gtagttttctcgagacctttggt-tgtcttttttaatcaagttttcttctggtgaagtatatgctaaactcttggaat--tttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
---tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| | || || |||| ||| | | | |||| | | || | | ||| | |||| | | || || | || || |||||||||||| |||||||||| ||| || |||||||| ||| ||| | ||||||||||||||||| ||||| ||||| |||||||||||||||| |
ccttcttcttctttataatttggttctt---tttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 1
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
|| | ||| | || | | | | | | | ||||| | ||| | || | || | ||| | | | | | | || ||||||| || | ||||||||||| ||||| |||||||||| ||||||||| |||||||| |||||||| || |||||| |||| || || || |||||
---gtagaagaaaagct---ttcttttgttctcgttgtctctattg--ttaaaactttggctgtttgttcctccctttgtctcttttgttgct--atcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA
upper sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 1
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttt-tctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
|| | |||| | || | | | | | | | ||||| | ||| | || ||||||| | | | | | || | || ||||||| || | ||||||||||| ||||| |||||||||| ||||||||| |||||||| |||||||| || |||||| |||| || || || |||||
---gtagaaggaaaact---ttcttttgttctcattgtctctattg--ttaagactttcgctg--ttttgttcctccctttgtctcttctgttgctatcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
ttctaac putative branch site (score: 1)
tttttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA