Sequence
atgc intronic sequence ATGC exonic sequence...aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
Basic information
species | Glycine max |
transcript | GLYMA04G32540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g54930.1 (Oryza sativa), 3'ss of exon 4
-----aaatgttgcct--tttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG---
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gtttgcaataatacctgttttataagctcgtgatttttttttcagcaccttgtaggcttgtacaaatagaattttctttctgattg--ggtttctttttta-----gATGAATGTGATCAAGGTTTCAAATATTATGGGGGTTAATCCAAAACCTTTTGATCCTGAAACATATGTGGAGGAGGATGCTTT---GACAGATGAATCTGGGA
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g38970.1 (Oryza sativa), 3'ss of exon 4
-aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaattttta---atctctctctca--tggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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taggctttac---taggaatgttatgatcgatgcttaaatgtttttgtgct---tttgcagctattcatatggttatttgttactgactaatttcttaacttgtagATGAATGTGATCAAGGTATCAAATATTATGGGGATTGACCCAAAGCCTTTTGATCCTAAAACATATGTGGAGGAGGATGTATTTGTTACAGATGAATCTG
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g01880.1 (Oryza sativa), 3'ss of exon 4
aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctca--tggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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taggcttgactaggaatatta-atgattggtgcttaaatattttgtgcttttgcagctattcatagatttttttg-ttactgactgatttcttaacttgtagATGAATGTGATCAAGGTATCAAACATTATGGGGATTGACCCGAAGCCTTTTGATCCTAAAACATATGTGGAGGAGGATGTATTTGTTACAGATGAATCTG
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G048494_T02 (Zea mays), 3'ss of exon 1
aaatgttgccttttgtaatg----atgtgcattctggtaagatatgttgaatttcaatattcaactactcatatttta-aatttttaatctctctct-catggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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----gttaattttggtgatatagcaaacacgttgtgtttagaacttttcatgcttggctaggaatt--ttattttccatgatcactaactgttttctattttgtagATGAATGTGATCAAGGTATCAAACATTATGGGGATTGACCCTAAACCCTTTGATCCAAAAACATATGTGGAAGAAGATGTTTTTGTTACAGATGAATCTG
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G019879_T02 (Zea mays), 3'ss of exon 4
--aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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tttcatgcttcactatg-aattttat-catccacaattgaaggtttgtgcttctgtagctactctcatattgattgatcattaactgttttctattttgtagATGAATGTGATCAAGGTATCAAATATTATGGGGATTGACCCTAAACCCTTTGATCCAAAAACATATGTAGAAGAAGATGTTTTTGTTACAGATGAATCTG
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
-----aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctgtagcaaaat-tgcgcttcctcatat----accgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g07160.t01 (Vitis vinifera), 3'ss of exon 4
-aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatt-tcaatattcaactact-catattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
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ctaatagtgccttcag--atcatctgatacttgtgaaagtctatcaatttatctgtcttgagctgtggcaaaattttaatattcaatagtact-ttgttacagATGAACATGATAAAAGTTTCTAATATAATGGGCATTGAACCAAAGCCATTTGACCCTAAAACGTACGTAGAAGAGGACACATTTGTGACAGATGAATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
ttttaat putative branch site (score: 3)
tttttaatctctctct CT-rich tract
aatattcaactactca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- -tgttgcc
- - - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactca