Sequence
atgc intronic sequence ATGC exonic sequencegtcggtcttgatttcaagtttcaaagttgtgctaattgctaaatgataaaatttatactccagcaattggctatggtctcttttttctatctgttctactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA06G24890.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 12
--------------gtcggtcttgatttcaagtttcaaagttgtgctaattgc-taaatgataaaatttatactccagcaattggctatggtctcttttttctatctgttc-tactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
|| ||| || | | | | | |||| | |||| | || | | || ||| || || | | | | ||||| || || | | || ||| | ||| ||||| | ||| ||||| | || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| || |||||||| | |||||| |
gttggttatcctatgttattctggagtcccatatcacaccttgtcattattgaatgaacattttagttaataacttgacagttttttttccttttcaatttctctccattgatgattaaaggtttggtaagctttcagGTGGATCGGAAATTAGTAAAACAGACAGTGATGACTTCTGTGTATGGTGTTACCTATATTGGTGCACGTGAGCAAATCAAAAGAAGATTGGCGGAGAAGG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20792 (Selaginella moellendorffii), 3'ss of exon 12
gtcggtcttgatttcaagtttcaaagttgtgctaattgctaaatgataaaatttatactccagcaattggctatggtctcttttttctatctgttctactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
| | | | || || |||| | || || |||| || | ||| | | ||| | ||||||||||| || ||||||||||| |||||||| ||||| || || || || |||| ||||| | ||||| | | ||| | |||| || |
--------------------------------------------------------------gtgagtatccatt-tcggttttctttacct-ttctcatcaattcttcggtca-----cagGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ32457 (Selaginella moellendorffii), 3'ss of exon 12
gtcggtcttgatttcaagtttcaaagttgtgctaattgctaaatgataaaatttatactccagcaattggctatggtctcttttttctatctgttctactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
| | || ||| | ||| | || ||| | | || | ||| | ||||||||||| || ||||||||||| |||||||| ||||| || || || || |||| ||||| | ||||| | | ||| | |||| || |
---------------------------------------------------------------------gtgagtatccatttcggttttctttacttttctcatcaattcttcggtcacagGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggctatggtctcttttttctatctgttctactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
ctctaaa putative branch site (score: 3)
ttttttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtcttgatttcaagtttcaaagttgtgctaattgctaaatgataaaatttatactccagcaattggctatggtctcttttttctatctgttctactctaaacttttgaaagtattcagATTGATAGGAAACTGGTCAAACAGACAGTAATGACTTCTGTTTATGGTGTTACTTATATTGGGGCACGGGAGCAAATTAAGAGAAGATTAGGGGAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA