Sequence
atgc intronic sequence ATGC exonic sequence...gtacttgaaactatgtgcctatcaattgttgtgcatttttttgggtgattccttgcaagttcaacttccatatgcaataataacctgtctctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG
Basic information
species | Glycine max |
transcript | GLYMA13G36140.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36140.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------gtacttg-aaactatgtgcctatcaattgttgtgcatttttttgggtgatt--ccttgcaagttcaacttccatatgcaataataacctgtctctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG
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gtaagtaactacctggttatacataccatattaatctgcttgtcactaaatgaactgttaatgcaatgttgagctattcggtatctttgtagaacatttattgagttgatggtttagacttcactaaatgatgagccttg---gtaaagatttgagatgcactaaaatggtacttttg-atacagGCGAAAAACATGAACCGCTGAGCTGGGATTTGAGAGTATATATTGCTTTAGACGTGGCACGTGGTCTAGAGTATCTTCATGATGGG
upper sequence: GLYMA13G36140.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G54590.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------------gtacttg-aaactatgtgcctatcaattgttgtgcatttttttgggtgatt--ccttgcaagttcaacttccatatgcaataataacctgtctctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG--------------
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gtaagtaactacctggttatacataccatattaatctgcttgtcactaaatgaactgttaatgcaatgttgagctattcggtatctttgtagaacatttattgagttgatggtttagacttcactaaatgatgagccttg---gtaaagatttgagatgcactaaaatggtacttttg-atacagGCGAAAAACATGAACCGCTGAGCTGGGATTTGAGAGTATATATTGCTTTAGACGTGGCACGTGGTCTAGAGTATCTTCATGATGGGGTAAGCTGCTTGCT
upper sequence: GLYMA13G36140.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 3
gtacttgaaactatgtgcctatcaattgttgtgcatttttttgggtgattccttgcaagttcaacttccatatgcaataa----taacct--gtctct--atattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG
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---gttga--cttggagacaatgtatt-ctgtgtattttccttttt--ccaccagcatataataatctcatggacaataacatgtaacttcaatttttgaacatgcagATGAGAAGTATGAGCCATTGAGTTGGGATTTGAGGATTTACATAGCTTTAGATGTGGCAAGGGGCTTGGAGTATCTTCATGATGGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|8286475|gb|BE024043.1|BE024043EST: TCCCACTTGTATA GTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAG
genomic: TCCCACTTGTATAgtaagttagc ... ctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAG
EST:
gi|18709588|gb|BM522441.1|BM522441EST: GCTTGTATATGTCTACATGAGTAAAGGGAGCTTGGCTTCCCACTTGTATA GTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAG
genomic: GCTTGTATATGTCTACATGAGTAAAGGGAGCTTGGCTTCCCACTTGTATAgtaagttagc ... ctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattccttgcaagttcaacttccatatgcaataataacctgtctctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG
taataac putative branch site (score: 1)
cctgtctct CT-rich tract
atatgcaataataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgaaactatgtgcctatcaattgttgtgcatttttttgggtgattccttgcaagttcaacttccatatgcaataataacctgtctctatattcagGTGAAGAGAATGGAGCTCTTGGCTGGGATTTGAGGGTTCATATAGCTTTAGACGTAGCAAGAGGCATAGAGTATCTTCATGATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
gtacttg
- - - - - -tatgtgc
- - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - ttgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtct