Sequence
atgc intronic sequence ATGC exonic sequencegttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
Basic information
species | Glycine max |
transcript | GLYMA06G36190.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 5
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttcca-atgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-----------------------gcatgc-acttctgttcacctagatcttttacatgctcgtcttagtttgtgattgatatttattagtgatgctaaacttttgcttaatttgcttgtagACCATAGCAGTGATCCAAGCTGGCCATGGCCTTCTTCAGCTTGGCTCTTGCAAGATC
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 5
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-----------------gcaagggagttgtttgattcacc--agccgaattttcatttgt-ctttataatcaatatagttttggtgacatttgtattttttttatctgctctg----cagACCATAGCTGTGATCCAAGCCGGGCATGGCCTCCTGCAGCTGGGCTCTTGCAAGATT
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-------------------------------------------gtaaatataatcaaacttcttttggttatatactgttc---ttgatcttaccttaacagtgttt--tatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 5
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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------------gtaaaataa-agaacactaatcat-atatgagaatgttcttg------actttcttgtttc------tcaagtcacctttgtaatcttttc--ttattgtacctacagACCATAGCTGTTATTCAAGCCGGACATGGCCTTTTACAACTTGGTTCTTGCAAGATT
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 5
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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gtcagaatcacagt-agtttgtggttttctattgttggtctttg--cgttatt----tgcattattgcttcttttctctgtcccttaattttgtcatctttgtat--gtcccttgaccagACCATAGCTGTAATTCAAGCTGGCCATGGCCTTCTTCAACTCGGTTCCTGCAAGATT
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05904 (Selaginella moellendorffii), 3'ss of exon 6
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgc-cagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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--------------------------------------------------------gtagctatccggaattctctttcttcacgggctctaagaacct-----tgtataccatctcgcagACCATAGCTGTGATTCAAGCTGGGCACGGACTTCTCCAACTAGGATCCTGCAAGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
tttattcc CT-rich tract
aatcatttcatttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA