Sequence
atgc intronic sequence ATGC exonic sequence...cctgactgattgctttatgcttatgcagcatcttcagcagcttttacattttaaatttgaactaatttgatattccatcactaactatggtttttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G38810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 6
--------------------cctgactgattgctttatgctt--atgcagcatcttcagcagcttttacattttaaatttgaactaatttgatattccatcactaactatggttt-ttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
|| ||| || | | || | | ||||| | || || | ||| | |||||||| | | | | | | |||| | | ||| |||| | || | |||||| | |||||||||||||||||||| | ||| || ||||||||||| | ||||
gtaggttttgcagaagaacacccatggaatttctgtgttctctcaagttacatctcttgttgcatt---gtattagagctgaactaa----aaagtttgttaa-atctattatctgttcgcagGGCATTGACAGGCATTATGGATGATTATTTTGATGGCTACTTTTCTGAAGAAATGATAGAATGTCAG
upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 6
--cctgactgattgctttatgcttatgcagcatcttcagcagcttttacattttaaatttgaactaatttgatattccatcac-taactatggtttttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
|| | | | | |||| |||||| | | | | |||| | | |||| || | || | || | || ||||| ||| | | || || | | ||||| || || |||| ||||||||||| ||||||||||||||||||
attctcatggttgatcaaactgttattaagcatccttatatcttctccttttttctttctaaactgatgccccttctaattaaatacttgtgattttt---agGGCACTGATAGGACTCATTGATGACTACTTCAATGGTTATTATTCAGAAGAAATGATAGAGTCTCAG
upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 6
cctgactgattgctttatgcttatgcagcatcttcagcagcttttacattttaaatttgaactaatttgat--attccatcactaactatg-gtttttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
| || | |||| | |||| ||| | || || ||| ||| |||| |||| || || || |||| || | |||| | || ||||||||| | ||||| ||||||||||||||||||||||||||||||||||| ||||||
--atataaatatatatatgtgtgtgcacacgctttgctcttgtgtatatggtaataatga-ttaatatgattaatatactctggaattatgtaaattactcagGGCTTTGATGGGCATTATTGATGACTATTTTGATGGCTATTATTCAGAGGAAATGATAGAATCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattttaaatttgaactaatttgatattccatcactaactatggtttttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
cactaac putative branch site (score: 1)
tttttccc putative PPT
ttaaatttgaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgactgattgctttatgcttatgcagcatcttcagcagcttttacattttaaatttgaactaatttgatattccatcactaactatggtttttcccagGACCTTAATGGGCATTTTAGATGATTATTTTGATGGCTATTATTCAGAGGAAATGATAGAGTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - tgattgc
- - - - - - -tttatgc
- - - - - - - - - - - -tgcagca
- - - - - - - - - - - - - - - -cttcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatcac