Sequence
atgc intronic sequence ATGC exonic sequencegtacttaacacatgatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
Basic information
species | Glycine max |
transcript | GLYMA06G03040.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 11
------------------------------------------------------------------------gtacttaacacat-gatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgt-tgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
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gtttgcatactggtcatcattttactattgtgttgacaatcattttgaggactttgttctttggaatatgtagtagtgatcccaaagagtttagagcaagtatttatattctgaaagc-cccaaaaatttacatatgtgataaagctgtatctgatgtctgtttcttattgcagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGCTATGTAATTATAATGATGGCACTCTTTTCAATCTATACAGGATTAATATACAATGAATTTT
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacttaacacat--gatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgttg-ttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
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---cttgacgtttctaaagatcagattagtctgttgcattttgatgttttgtgcttacaagttctagatgctaacctcttcaatcgttgcttcctgacaacagAAACTTGGGGATATTATGGAAATGGCTTTTGGTGGGCGTTATGTCATTTTGATGATGTCACTCTTCTCAATATACACTGGATTAATCTACAACGAGTTCT
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 11
gtacttaacacatgatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccag---tgtcagttttgtttaat--gttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
|| | | | | || || | || ||| || ||| | ||| ||| | | | |||| | ||| | || || | || ||||||||| |||||||| ||||| ||| | ||||| || || ||| | |||||| ||||||| || |||||||| || || || ||||||||||| || || |
---atttccttgtacattttgagtcttagctttacttcttaac--caattttcagtttgatggttgatctattagttcagcttacttgatttttgttgactgcagAAACTAGGAGACATCATGGAGATGACTTTTGGTGGGCGTTATGTGATTATGATGATGGCACTGTTCTCAATATACACAGGATTGATATATAATGAATTCT
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ10256 (Selaginella moellendorffii), 3'ss of exon 10
gtacttaacacatgatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
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--------------------------------------------gttcgtttggttttcctctt--cttcag---tgttttattctgagcttaaaaacagAAACTGGGAGACATCATGGAAATGGCATTTGCCGGTAGATACGTGCTGCTTCTCATGTCTCTTTTCTCAATCTATACGGGCTTCATCTACAACGAATTTT
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 10
gtacttaacacatgatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
| | ||| |||| | ||||| || | | || |||| ||| ||||||| |||||||| |||||||||||||||| ||| | || | | | || ||| | || |||||||||||||| || || || || ||||| ||||
--------------------------------------------gttcgtttggttttcctctt--cttcagtcttttattctgagcttaaaaac---agAAACTGGGAGACATCATGGAAATGGCATTTGCCGGTAGATACGTGCTGCTTCTCATGTCTCTTTTCTCAATCTATACGGGCTTCATCTACAACGAATTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccttttatttttatgccagtgtcagttttgtttaatgttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
taataac putative branch site (score: 1)
ttttgtttaatgttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttaacacatgatcatggggtatttgtattgaatctgaatgttcccttttatttttatgccagtgtcagttttgtttaatgttgttaataacggcagAAACTTGGAGACATAATGGAAATGGCATTTGGCGGACGCTATATCATTATGCTGATGGCCCTCTTCTCAATCTATACCGGGTTGATATATAACGAGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT