Sequence
atgc intronic sequence ATGC exonic sequencegtatgcattctattcccacatgttgcctatttaagtgcatgtttgttttttatttgattggccttttggaaaaatctctcatattcgtttttcttgcagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
Basic information
species | Glycine max |
transcript | GLYMA03G40220.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcattctattcccacatgtt-gcctatttaagtgcatgtttgtttttt-atttg-attggccttttggaaaaatctctcatattcgtttttcttgc-agGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
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gtatgtacttcgaacccatgacttagagcattttgttacttataggtgcattgatttgtgtttgggtcttaaatttttctcatcttttttttttctttattagGACCCTTTTTTAAGAATATCTAGGATTGTTGAAAATGGAGGTTCTGTTCCAATTTGCAAGACAGAAGTGGTTGATAACAACTTGAATCCAATCTGGAGGC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcattctattcccacatgttgcctatttaagtgcatgtttgttttttatttgattggccttttggaaaaatctctcatattcgtttttcttg--cagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
||||| | | ||| | | | |||| | | ||| | || || | || |||| || ||| | || ||| || |||||||| ||||||||||| |||||||||| || || ||||| | |||||||| |||||| || |||||||| ||||| | || |||| || ||||||| |||| |
gtatgtacttagaaccctgacttagagcattttgttacttgtgtattgatt-tgtgtttgggtctt---aaatttttcacatctttttttttctttattagGACCCTTTTTTAAGAATATCTAGGATTGTTGAAAATGGAGGTTCTGTTCCAATTTGCAAGACAGAAGTGGTTGATAACAACTTGAATCCAATCTGGAGGC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcattctattcccacatgtt-gcctatttaagtgcatgtttgtttttt-atttg-attggccttttggaaaaatctctcatattcgtttttcttg--cagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
||||| | || |||| || | |||| | | | | || || ||||| || | | || | |||| | || |||||||| ||||||||||| |||||||||| || || ||||| | |||||||| |||||| || |||||||| ||||| | || |||| || ||||||| |||| |
gtatgtactcagaacccatgacttagagcattttgttacttataggtgcattgatttgtgtttgggtgttaaatttttctcatctttttttttttctttattagGACCCTTTTTTAAGAATATCTAGGATTGTTGAAAATGGAGGTTCTGTTCCAATTTGCAAGACAGAAGTGGTTGATAACAACTTGAATCCAATCTGGAGGC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcattctattcccacatgttgcctatttaagtgcatgtttgttttttatttgattggccttttggaaaaatctctcatattcgtttttcttg--cagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
||||| | | ||| | | | |||| | | | || || | || || | | ||| | || ||| || |||||||| ||||||||||| |||||||||| || || ||||| | |||||||| |||||| || |||||||| ||||| | || |||| || ||||||| |||| |
gtatgtacttagaaccctgacttagagcattttgttacttattggtgtattgatttgtgtttgggtcttaaatttttcacatctttttttttctttattagGACCCTTTTTTAAGAATATCTAGGATTGTTGAAAATGGAGGTTCTGTTCCAATTTGCAAGACAGAAGTGGTTGATAACAACTTGAATCCAATCTGGAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttttatttgattggccttttggaaaaatctctcatattcgtttttcttgcagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
atttgat putative branch site (score: 5)
tctctcatattcgttt putative PPT
ttatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcattctattcccacatgttgcctatttaagtgcatgtttgttttttatttgattggccttttggaaaaatctctcatattcgtttttcttgcagGACCCTTTTCTAAGAATATCAAGAATGGTTGAGACTGGAGGTTATGTTCCTATATGCAAGACTGAAGTTATCGACGACAATTTAAATCCAAAATGGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG