Sequence
atgc intronic sequence ATGC exonic sequence...catatttgatctaacattataattattatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
Basic information
species | Glycine max |
transcript | GLYMA11G07990.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
catatttgatctaacattataattat-tatttgatctaatgttagcaa---tagatc---tgagttagtttt-tattc-ttttttttgctgatgt---gaatgatatggcagAGAGA-----TGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
||| || | | | ||| ||| || || || | ||| ||| |||||| ||| ||| | | ||| | | || | ||| || || ||| |||| |||||||||||||| || ||||||| |||||||| ||||||||| |||| || | ||||| || || ||||| || || || || || || ||
---gtttaattaatcttcatacatatatacttaatttcatgcatgcatagctagatcaatcgagctagctatatatagatcgatgctgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT
upper sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
catatttgatctaacattataatta-ttatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
||| ||| | || | | | || | || ||||||| || | | | | | || | |||| ||| | || || ||||| || || ||||| |||||||| || || ||||| || || || |||||||| |||||||||||||||||||| |||||
---------------------gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaatttta-aatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
upper sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
catatttgatctaacattataattattatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatg-gcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
|| | ||| || ||| || || | |||| ||||| ||| || || | | | | | | ||||| | | ||||||||| ||||||||||| || ||||| | |||||||||||||||||||| | ||| || |||||||| || ||||| || || || |||| ||| |
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgt-agctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
upper sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G36160.1 (Arabidopsis thaliana), 3'ss of exon 2
---catatttgatctaacat-tataattattatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctga-tgtgaatgatatg----gcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
| || | || ||| ||| | | ||| | | | | |||||| | | | || | | | || ||| | ||| || | |||||| ||| | || || ||||| || ||||| |||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||
gttttcacaaaatacatgatgcatacttaatttaggatttttttcttcttcttaatctga--caatgtgaatacatagatctgatgagcattaattatgtatattatagAGAGCTGCCGAATCGGATATGAGGAAAGAAATGAATGGTATTTCTTCAGCCACAAAGATAAGAAATATCCAACAGGAACAAGAACAAACAGAGCGACCAT
upper sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
catatttgatctaacattataatta-ttatttgatctaatgttagcaa-tagatctgagttagtttttattctt----ttttttgctgatgtgaatgatat--ggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
|||||| | | || | || | | | || || ||| | | ||| | | | |||| ||||| ||| | ||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| || || |||||||| |||||
--------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatagatctgagttagtttttattcttttttttgctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
tgctgat putative branch site (score: 3)
agttagtttttattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatttgatctaacattataattattatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgagtt