Sequence
atgc intronic sequence ATGC exonic sequencegtaatatattatcttcacttctgcttgcgaagaaaatacaaaactaaaaaaagagaaaaagaaatcttaacttttgttctagtggcctctaaatagacagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
Basic information
species | Glycine max |
transcript | GLYMA08G21840.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21840.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 7
gtaatatattatcttcacttctgcttgcgaagaaaatacaaaactaaaaaaagagaaaaagaaatcttaacttttgttctagtggcctctaaatagacagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
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-------------------------------------------------atgtgttactttaagcctttaattttgttttaggagtcac---atacaatgcatcttgtgtcaaaatttcttccatgctaatatatattctctgaggttgcagGTTGAGTTCATGCCGAAATTTAGTGTGAGGGGAATATGGCAGAGGTGGCGTGAGTCATATCCCAACAATGGCAGTAAAAATGATGAAGCAATTACAGTAT
upper sequence: GLYMA08G21840.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G16170.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatatattatcttcacttctgcttgcgaagaaaatacaaaactaaaaaaagagaaaaagaaatcttaacttttgttctagtggcctctaaatagacagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
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------------------------------gtaacttatactattgagatttgctttggctagctctt---tcaaaatacattaccttcggaaaacatcaggctagttttaggtttttaattg-------attttcacattcctttttcaagGTGGAGTTTTTGCCCAAATTTAGTGTTAGTGGAATCTGGCGTAGATGGCGTGAATCATATCCGGTGAATGATGAAAAAACCAACGACTCCATAACTGTAT
upper sequence: GLYMA08G21840.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 3'ss of exon 7
gtaatatattatcttcacttctgcttgcgaagaaaatacaaaactaaaaaaagagaaaaagaaatcttaacttttgttctagtggcctctaaatagacagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
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----------------------------------------------tcattttttcatctagattgctcatttactctacaaggcttgttcactaatctaagttcagtttaattatttggttgtaat---atatttattt---ttattgaagGTTGAGTTTATGCCCAAGTTCAGTGTGAGAGGAATCTGGCAGAGATGGCGTGAATCACATCCTAAAGATGGAACTAAGGTTGATGATGCTATAACCGTGTMapped 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|18039709|gb|BM308003.1|BM308003EST: TTCATGGGTTTTTCAATGGTTTAATGGCCCCTCTCTATGCAGGCTCCACG GTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGT
genomic: TTCATGGGTTTTTCAATGGTTTAATGGCCCCTCTCTATGCAGGCTCCACGgtaatatatt ... cttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
atttaat putative branch site (score: 4)
ttgtctt CT-rich tract
attttaaatatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatattatcttcacttctgcttgcgaagaaaatacaaaactaaaaaaagagaaaaagaaatcttaacttttgttctagtggcctctaaatagacagtatccattttaaatatttttttgtggctaagaatttaattgtcttgttgaagGTTGAGTTTTTGCCAAAATTTAGTGTGAGAGGAGTTTGGCAGAGATGGCGTGAGTCATATCCAACTGATGGTTCTAAGGCTGAAGATGCTATAACTGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG