Sequence
atgc intronic sequence ATGC exonic sequencegtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA06G12410.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G12410.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g08950.1 (Oryza sativa), 3'ss of exon 8
gtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
|||||| | | || | |||| || | ||| | || || | | || || ||| | ||||| || ||| ||||| ||||||||||| ||||| |||||| | ||||| || ||||| || |||||||| || || || |||||||| || ||||| || ||||||| | ||
gtttgttagctaattgattgtttg-ctatttcacctttttttt-------tgttg--ggttgtggcaacctta-------ccttaccagtgtat-gcatatcttt-tgcagATACTTGGCTCCAGAATATTTCATGCATGGCAAGGTGAATGACAAAATTGATGTATACGCTTTTGGTGTCGTCCTTCTTGAACTCATTTCAGGCAAGAAA
upper sequence: GLYMA06G12410.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G032337_T02 (Zea mays), 3'ss of exon 7
gtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
|| || | || | | || ||| | || || | || ||| ||| | | | | | || | || | |||| |||||||||||||||||||||||| | ||||| || | || || ||||| ||||| |||||||| || || || ||||| | || || || ||
---------gtttgtttcttaacaattgttttattgtttttccgtctgt-tgtagc----attggagcaattg-------ctttactgacatag---agatatcttggcagATACTTGGCTCCTGAATACTTCATGCATGGCAAGGTGGGCAACAAAATCGATGTGTATGCTTTCGGTGTTGTACTTCTGGAGCTCATCTCTGGCAGGAAA
upper sequence: GLYMA06G12410.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
| || | ||| || || | ||| ||| | | | | || | || ||||| || | || | || | ||| ||||| ||||||||||| || ||||||||||| || || || ||||||||||| ||||| ||||||||||| || || ||||| ||| | ||||| || |||||
-------------------gtatgaa-gtac--tctaggttttgggta-atgtttc--atgaaagttc-ttgaaaatgttcttgtgcta-atcttctgtt--tttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
upper sequence: GLYMA06G12410.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g01680.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------gtttgtacttttaaaccctgcataactataccatcccct-ttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaatta-tgtattacactcattta---tgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
| | || || ||| || || |||| | | | ||| | | | | || | | | | | ||| | |||| ||||||||| |||||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||||||||| || |||||
gtttgtgcttcttctctagtagctataacttctatgtcccacattcttgtcatttttcagaagatcaataaaccccactattttgaattatggctttaaaatcttgagtaaaaaagttattacttgtcattgagaaagttcagaacatttattttctctgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGAGAAGATAGATGTCTACGCATTTGGTGTTGTCCTCCTTGAGCTTCTTTCGGGAAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
tcctaaa putative branch site (score: 2)
ctcattt putative PPT
taaattatgtattaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA