Sequence
atgc intronic sequence ATGC exonic sequencegttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
Basic information
species | Glycine max |
transcript | GLYMA02G39040.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 6
---------gttagcatttttccatgttcattttcttg---gtattttattt---tggggggac---tgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
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gtattgatagtaaagagtcctttaatcttgtgattctgactatattttactcacatacacacatctttagttggggtccaattgaattatcttcgtgttaattttctctgaatctacc-tagGAAATGGATGGATTTGACACCAACTCAGCTGTCATTGTACTTGGAGCAACAAACCGAGCAGATGTTTTAGATCCTGCCCTCCGACGCCCTGGGAGATTTG
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
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------------gtaagtctgctgtcaagcacctttcctgtgtaagta-----gcattcttgatctttccatgacccattcacatgttggaaacttttctgcagGAGATGGATGGTTTTGACAGCAATTCTGCGGTTATCGTTCTTGGAGCTACAAATCGTGCCGATGTCTTAGATCCGGCCCTGCGTCGTCCTGGGAGATTTG
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
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------------gtaagtttgtaattatg-cacttt-tcctgccagagttgctttcttgatctttg---cattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 6
gttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtc-ttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
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----------------gtaggtttctcctggaagttatctttcagcttctgaaat-gttttaaccatttccttgttagtttaatgtgattgaaattgggctgcagGAAATGGATGGATTTGATAGCAACTCTGCTGTTATTGTTCTTGGAGCAACTAATCGTTCAGATGTCTTAGATCCTGCACTTCGCCGCCCTGGGAGATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
gtctaac putative branch site (score: 2)
tcttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT