Sequence
atgc intronic sequence ATGC exonic sequencegtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
Basic information
species | Glycine max |
transcript | GLYMA06G44340.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g48640.3 (Oryza sativa), 3'ss of exon 13
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcac----ttcccattatcattgc-gcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
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-------------------------------------------------gttagttatgcgaatttcatcaaaggtttccagggcaagcaaggttctcaacattcttgttgcagGATAAACTCATGACCACACCATCAGATTCTTCAAGCAGTGGTTCTTCTGGAAACTGGTTATTCAAGAACAAGGAACATGGGAAAGCTAGTGCAGCCGCTA
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 13
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcac----ttcccattatcattgc-gcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
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-------------------------------------------------gttagttatgcgaatttcatcaaaggtttccagggcaagcaaagttctcaatgttcttgttgcagGATAAACTCATGACCGCACCATCAGATTCTTCGGGCAGTGGTTCTTCTGGAAACTGGTTATTCAAGAACAAGGAACATGGGAAAGCTAGTGCAGCCGCTA
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 13
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
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-------gttagctctacaaacaatatgttacttttagt-tctttccgaggaaagaatgaatctcaagaccatatcttct-----------------------gtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGAAACTGGTTATTCAAGAACAAGGAACATGGGAAAGCCAGCGCAGCAGCTA
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA---
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----------------------------gtatgattacaggatcttaatgtgcaacataagaagaactttggaagctgcc-cttttcatat---atttccttattgcagGACAAATTAATGACAGTACCATCTGAC---TCAACCAGTGGATCGGCTGGAAACTGGCTCTTCAAAAATAAAGAACATGGAAAGACCAGTGCAGTTGCTAGTC
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA---
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-------------------------------------gtatggttgcagatta-taataaaatagatctagtggaagacgtgtcctcttaatatatttgcttatcgcagGACAAACTAATGACAGTACCTTCAGAC---TCAACCACCGGATCTTCTGGAAACTGGCTCTTCAAAAATAAAGAACATGGCAAGACTAGTGCAGCTGCTAGTC
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 13
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctctt-ctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
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gtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattca-ttggtttttccttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGAAATTGGCTTTTTAAGAATAAAGAACATGGGAAAGCCAGTGCTGCAGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
ttctcac putative branch site (score: 2)
attatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcagGATAAATTAATGACTGTTCCATCAGATTCTTCAAGCAGTGCTTCTTCTGGAAATTGGCTTTTCAAAAATAAGGAACATGGGAAGACTAGTGCTGCAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT