Sequence
atgc intronic sequence ATGC exonic sequence...atggcagattaatccccctagtatgttgtgtcaactaacattcttttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA04G38360.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------atggcagatt---aatccccctagtatgttgtgtcaactaacattcttttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
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gtatcttttaagaacttagactatttagaatctcctcagtcctcaatggatgtttcaggtgctaaaattacaaaatgcagacaatgatactacaatggtcttcaattttttttttgtgcatatacctgaatc-cttattcttgtttgtctatgggtttcagTTATTATGATCCATACAGAGGTGTAATTGTATATTTTCGAGTTGTTGATGGCAGTATAAAGAAAGGGGACAAAATATGTTTTATGGCTAGCGGAAAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 8
atggcagattaatccccctagtatgttgtgtcaactaacatt--cttttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
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----------gttccctttaagtacttgagctctttagaactggctaattaatgttatacatgtatctgaactattgctatatgttgtctttgtggttgcagCTATTATGATCCATACAGAGGTGTAATTGTGTACTTCCGTGTTATTGATGGCAGTATGAAGAAAGGGGACAAGATATGTTTTATGGCCAATGGAAAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 8
atggcagattaatcccc--ctagtatgttgtgtcaactaacattc---ttttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
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gtgaaatactcgtgtttgttttgcttgattagtctacaagtgtgcagtttttatatgtgaac----tactttatat-ttttcgtccaaaattcattttgctgcagTTATTATGATCCATATCGTGGTGTCATTGTATACTTTCGAGTTATCGATGGGAAAGTGAAGAAAGGCGACAGAATTTTTTTCATGGCAAGCGGAAAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 8
atggcagattaatccccctagtatgttg-tgtcaactaacattcttttacatgcggtatttatacttcatgcactcatatttattatttctttaca----tgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
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-ttcttttgttttctctttgctattttaatttcagcatataacatattagcctttgcatta----tttgggtgtgtataaatatcatttcttcaaaccttttcagTTACTATGATCCATATAGAGGAGTGATCGTATATTTTCGAGTCATTGATGGGACTATAAAGAAAGGTGACAGGATTTATTTTATGGCTAGCAAGAAGMapped 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|16282790|gb|BI945208.1|BI945208EST: CCACCTGAAGATACATCTAAAAAACCATTGAGGACTTTAATATTTGACAG CTACTATGATCCAATATAGAG-TGNTATTGTATACTTTCGAGTT
genomic: CCACCTGAAGATACATCTAAAAAACCATTGAGGACTTTAATATTTGACAGgtactcttca ... ttacatgcagCTACTATGATCCA-TATAGAGGTGTTATTGTATACTTTCGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
tttattatttcttt CT-rich tract
tcatatttattatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggcagattaatccccctagtatgttgtgtcaactaacattcttttacatgcggtatttatacttcatgcactcatatttattatttctttacatgcagCTACTATGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - -atccccc
- - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcac