Sequence
atgc intronic sequence ATGC exonic sequencegtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
Basic information
species | Glycine max |
transcript | GLYMA19G45050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 3
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
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-----------------------------------------------------gtgaacagaatt-----gacgcccttaattttctatatgactcacattttctgcatttgctaat---------ttgtctaacgtacaaccttgtgttgttcgcaac--cagGAACCAGTTCTTCCTGGTTCATTCCTCCGAGCCAGGGCCATTGGTCTCATGCCTATGATTGACCAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 5
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatg-tagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgt-tatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
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-----------------------------------------------------------attagtcctctggc---tgtcacactctcagactgatcaactgctcta----gttgcatcagcttcagttatttgtcactgacatttttatggtttatgtcctgtagGAGCCTGTTGTTCCTGGTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttg---aatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
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-------------------------------------------------------------------------------gtaactgtgt--tttcacaaccatcaaaattatcatcaaataccacattgtgttgtaacctgagttagcttctgattcgt----gtagGAACCAGTGCTTCCCGGATGTTTCCTCCGTGCTAGAGCCATTGGATTAATGCCCATGATTGATCAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
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----------------------------------gtagttcaaactagatagcatttaatcaataataagagctcgtctttg-ttttgcaact--aaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactg-----acatttttg-aacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 4
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgtta-tgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
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-----------------------------------------------------------------------------------------------------------------------gtagtgttctttttgtaagacgaagttactacggtgggggtttcagGAGCCTGTGTTGCCTGGATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
atttaat putative branch site (score: 4)
tatttaattaagaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG