Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcattattttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
Basic information
species | Glycine max |
transcript | GLYMA18G10460.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 6
gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcattattttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
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---------------------gtaagctttgtatcgccaaatgt---tttagcgtcaatgcaacttccatt--ctcgcccttcttattgc-cttaaaatttccagGTCATTGCATGTCTTGATGTTCGGTCAAATGATAGTGGGGATCTTGTGGTAACAAAAGGTGACCAGTATGATGTAAGAGACCATAGTAGTAGCAAAGAG
upper sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcattattttgatttcctgacaaaacattgttta--ttaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
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gtaagaagtttgtcctgttattattgaaagtctgcctcctttgcaacattgcta------tctttgc-tcttaactat-tctggtaggcagtttttctaatgatattttgttttcctttagGTGATTGCTTGTCTTGATGTGAGGACGAATGATAAAGGAGATCTCGTAGTTACTAAAGGGGATCAGTATGATGTGAGAGAGCAATCTAATGAAAACGAG
upper sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------gtaatagtcatggaaatcctcttgt-gctttaaattagttaatgtgttcttcgcctctggggtgc--attcattattttga-----tttcctgacaaa--acattgtttat-taagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
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gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
upper sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcatt---attttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
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ttgaaaggaccggaa----tctgtcgtttcaa--taattcat-tgtcctttttctgaagatcggaacgacagaaatctcactccgttcacgtcgtattgtatggca-gGTTATTGCATGTCTTGATGTTCGAAGTAACGACTCAGGGGACCTTGTTGTGACTAAAGGTGATCAGTATGATGTACGAGAACAATCTTCAGCACGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcctctggggtgcattcattattttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
tcctgac putative branch site (score: 2)
attcattattttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtcatggaaatcctcttgtgctttaaattagttaatgtgttcttcgcctctggggtgcattcattattttgatttcctgacaaaacattgtttattaagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA