Sequence
atgc intronic sequence ATGC exonic sequence...atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
Basic information
species | Glycine max |
transcript | GLYMA09G06640.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
--------------------------------------------------------------------atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttg------atttattt---aagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
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gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttc-tatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G099452_T02 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------------------atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
| || || | | || | | ||||| |||||| | | | | | || | | || || | | | ||| | ||||| || || ||||| ||| | ||||| ||||| |||||||| || ||||| ||||| ||||| || |||||||||||||| | ||| | |||||||| |
gtaagctttgtatgtagatctctttttcctcaaggaagcacccatgtgattatcgccagcattttagttctgcgcttttgccgtccttttgcatattttgtggactagtgattcttga----ggatatctttctgtgcttga-accaattcaaaattgttgtggtaatattttc----gcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCTGCGCCGCATATTGCTGGCATTGCAGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC
upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------atgattaagcg-tggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagcagtttttcc------ttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
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gtaagcgtgcgttgtctgtagacctcttcccctcgaggaagcacccatgattaccatcagtattttactactgcgctcttgccgcccttgtgcatatcttctggattagtgatcggtggtgatatttttctgtgctcgaaccaactcaacattgctgtggtaatatttctcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCCGCACCGCATATCGCTGGCATTGCGGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC
upper sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagc--agtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
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-gaatttgaaaaccatgccagcaggataacatgctatagttactgt-acttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGCMapped 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|8670427|gb|BE191534.1|BE191534EST: GATTTGGGCTGCATGGTCTCTAAATGGAACTGATGAGCCAAATTATGCTG GAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAG
genomic: GATTTGGGCTGCATGGTCTCTAAATGGAACTGATGAGCCAAATTATGCTGgtaagtaatg ... ccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcatcagtatactataaaatttgatttatttaagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
atttgat putative branch site (score: 5)
tttttccttgt putative PPT
tatactataaaatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - -cacttga
- - - - - - - - - - - - - - - - - - -aaaagata