Sequence
atgc intronic sequence ATGC exonic sequence...ttaaacaatccataaaaggaaaaattttctttgacataatgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G15820.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 10
ttaaacaatccataaaaggaaaaattttctttgacataatgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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-----------------------gtacattttgat-tgccttttaactaggcatatatttgcattgtcataagctgattgaatatttttgcattgtttagGGTGATACACTTCAAAGGTGGAGAACAGAGCCGTATATCATGATAACTGGTAGTGGAAG
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 10
--ttaaacaatccataaaagg---aaaaattttctttgacataatgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaa-tgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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agttttccatcatgtaaaggttctggagatttctgtttatgcattctatcaatgtgga------acaatggatcactgattattttttatgcctctctaaatgcagGGTGATACTCTTCAAAGGTGGAGAACTGAGCCTTTCATCATGATAACTGGCAGTGGAAG
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 10
--------ttaaacaatccataaaaggaaaaattttctttgacataatgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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aactggtgctctatagtttccaaaagggagagttgtaggtg-taca-tctagtggga-agttctgttcgagctg---attgacaagggtgtgacgg--tgaattgtagGGAGATACGCTTCAAAGATGGCGGACAGAGCCTTTCATCATGATAACTGGGAGTGGGCG
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 10
----------ttaaacaatccataaaaggaaaaattttctttgacata-atgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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gaccgttactctaaatattccaaaagaagagag-----tgatgatgtacacctagtgg----ggagttctggatgaactgattgacgaggttgtaatgg--tgcattgtagGGAGATACGCTTCAAAGATGGCGGACAGAGCCTTTCATCATGATAACTGGGAGTGGACG
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ16538 (Selaginella moellendorffii), 3'ss of exon 9
-ttaaacaatccataaaagga---aaaattttctttgacataatgttgtgatatagatgtttttgaat--tggtga--ttgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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gtatggcttactggggtggggtttatagttttcattttcttga-gctttttcatgcctggttatgattgctggacaatctgacgagtagtttcttatatgaaatgtagGGAGACACACTTCAAAGATGGAGGACAGAGCCTTTCATCATGATCACGGGTAGTGGGCG
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32251 (Selaginella moellendorffii), 3'ss of exon 9
ttaaacaatccataaaaggaaaaattttctttgacataatgttgtgat-----atagatgtttttgaat--tggtga--ttgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
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--gtatggcttactggggtggggtttgtagttttcattttcttgagctttttcatgcctggttatgattgctggacaatctgacgagtagtttcttatatgaaatgtagGGAGACACACTTCAAAGATGGAGGACAGAGCCTTTCATCATGATCACGGGTAGTGGGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
gattgac putative branch site (score: 3)
tttgcct putative PPT
tttttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaacaatccataaaaggaaaaattttctttgacataatgttgtgatatagatgtttttgaattggtgattgacaatgtgttatttgcctgtaatgcagGGTGATACTCTTCAAAGATGGAGGACTGAACCTTTTATCATGATAACGGGTAGTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - -caatcca
- - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg