Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
Basic information
species | Glycine max |
transcript | GLYMA20G35110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
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-------------------------gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttc-taaacg-------------tctttttttctcca-atgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
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--------------------gtctagtgaagcaatcaac-tatctgagtaaatttgtagcgtatcatttttcttttt--tggtgttctgaccatcca----tttacttctccaatttgttacagAGATATCAAGCCTGATAATCTGCTACTCGACAGAAGCGGTCACATGAAGTTATCCGATTTTGGATTATGTAAGCCATTAGATTGTAGTATTCTCCAGGAA
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctcaagctgcaaatagtcatgttacaccatg-aaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaa--aagatataatattctaattttgatatgc--attccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
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-----------------------------gtttgtgtaagattttatcatgattgtatgtgggaaccatatgcatgcttctgatcatgacttaagaagcaataaccctctccatatttacttattacagAGATATCAAGCCCGACAATTTACTGCTCGATAGATATGGACATATGAAATTGTCAGATTTTGGATTATGTAAACCATTGGATTGCAGTAATCTTCATGAG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattt----tgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
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-------------------------gct-tggtatgaaggactctctcgtgttcactgatg--cctgtttatttgaaattgatgttccgcttacttttgactccaacatctactggtttgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCC
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 4
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattc----cagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
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-------------------------------------------------------------------gtatgttgcgagtcgagaacatg-gcttgaacttaccagtttttctgtgtcttctgtgcagGGATATCAAGCCTGATAATCTTCTACTTGATAAGAATGGTCACATGAAATTGTCAGACTTCGGGTTGTGTAAACCCCTAGACTGCTCTAACTTACCAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
acataaaaaaaaaaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG