Sequence
atgc intronic sequence ATGC exonic sequencegtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
Basic information
species | Glycine max |
transcript | GLYMA12G03260.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 6
gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
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--------gtgggacatgttatttgatgtcccatgtgtcaagtcatgagtt---ttcatctaaatgttttttttcctgttatagGATGACGGGGAGATGTATGATGAATTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGAC
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 6
gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
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----------gtgggatatgttatttgatgtcccatgtgtgaa---gtcttaggtttgcgtctaaatgttgctttcgttg-tagGATGACGGAGAGATGTATGATGAATTTGGCAACCTCAAAAAGAAATTTCGTGCTAAAACACAACAAACTGAAAATGCACCAACTCTTCCTGGGTCTGGAC
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGT--TCAGGGC
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gtaagatatgcttttcctgaagagttctttgttttttgtttttttgttgcaattcggatgagctctcagttt-tttgtatattccatttgacttata-cgtctaatatattt-cagGATGATGGTGAAATGTATGATGAGTTTGGGAATCTAAAGAAGAAGTACCGTGTTAAAACAAACCAAGCTGACACCAGACCTGCTGTTGCTGCTGGTCGTG--
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 5
gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactgg---cagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
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----------gtaagataaatgtgtacaagctatatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGCMapped 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|10256086|gb|BE823852.1|BE823852EST: NTGATGAAGAGGAAATAGAAGAAACTAGACGTCGTAGGAGNGAAGCNNAA GATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGT
genomic: TTGATGAAGAGGAAATAGAAGAAACTAGACGTCGTAGGAGGGAAGCTGAAgtaagattga ... ttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
tcctttttact CT-rich tract
atatatatatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactggcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC