Sequence
atgc intronic sequence ATGC exonic sequence...tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
Basic information
species | Glycine max |
transcript | GLYMA10G43480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 1
tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctca--gGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| ||| | | | | | | || || || | || | | || |||| ||| | ||| | ||| ||||| || ||||||||||| || ||||| || |||||||| ||||| || || || ||||||||||| ||||| || || |||||||| |||||||
--agtgttgaaacttgtagtagcagccgtcttcttcttttttcatgacaatgatttgctaagatactctggtaattcacaagatattttgactattatatagGTGAAAGAAATTCTTATTGAGGAATCAAATGTACAACCTGTCAACAGTCCTGTCACCGTCTGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAAC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 1
---tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataac-aaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| | || || | || | | | ||| || | ||| | | || |||| | | | | | || | ||| ||||| |||||||| || ||||||||||| || || |||||||| || |||||||| || || ||||||||||| ||||| || || |||||||| ||||| |
agataccattttatggtctcc---tttctcagcgattgatttatagatttgcgaagatgaatcatggtgttaaccagaagatgtttatcataatgttata-cagGTGAAAGAGATTCTGATTGAGGAGTCAAACGTACAGCCTGTAAACAGTCCAGTCACCGTATGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAGC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 1
--------------tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
||| | |||||| | ||| | | || | || | | | | || ||| | | | | | | ||| || |||| |||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||
ttctaggcaaaaaacacatttgggtgtt-ttaaacaacactgaataa-gttttatagctgcctccatgcttatctgatgactgatatatgttctatattt------------agGTAAAAGAGATCCTCATTGAAGAGTCTAATGTTCAGCCTGTCAATAGTCCAGTCACTGTTTGTGGTGATATTCATGGCCAGTTCCATGATCTAATGAAAC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 1
tgcatcttggtgttatcaaaatatgt---tttatgctgacttgcatattcttttatttctattga-accaataacaaacgttttagatt-tttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
|| | ||| |||| || | | | | | | || | | | || | || || | | | || ||| ||| ||||| ||||| || | | ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || || ||||| | ||||| |
-----ctctgcgtttgagaaattagtccttctttatggttatacgaatggtctcgctggcatcggtgttcatgactttcatcaaactttgttttgttcatcgcagGTGAAAGAAATATTGGTGGAGGAATCCAATGTTCAGCCTGTCAACAGTCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 1
------tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
||| || | | ||| | || | || ||| ||| | || | || |||| | | || | | ||||| ||||| || | || |||||||||||||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||||| |
tgccgtcagctctatttggttgtgcgaggggttatcagcgcagatggcctctctggcattgtttttcattgctcaataaactctct------tttgtctcccgcagGTGAAAGAAATATTGATGGAGGAGTCCAATGTTCAGCCTGTCAACAGTCCTGTTACTGTTTGTGGCGATATTCATGGACAATTTCATGACTTAATGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
caataac putative branch site (score: 2)
ttttagatttttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcatcttggtgttatcaaaatatgttttatgctgacttgcatattcttttatttctattgaaccaataacaaacgttttagatttttgaaatatctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
- - -cttggtg
- - - - - - - - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - -ttgcata