Sequence
atgc intronic sequence ATGC exonic sequencegtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
Basic information
species | Glycine max |
transcript | GLYMA13G11700.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctct-ttaatttgcttttgcatattactaagacacttgttac----atttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
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---------------------------------------------------gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctga--ttactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
||| | || | | || || | ||| || | | |||| ||| || ||||||||||||||| ||| || |||||||| || ||||| |||||||| || |||||||||||||| || ||||| || || || ||||| |||||||| || |
-------------------------------------------gtaagattctatcagaggtccagaacat-------tatagccttagagggttgactttatttccatttcatatgacc-tacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
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-------------------------------------------gtaagtaagacta--ctactagaagtcgagaacattgtagccttagagttctcacttcatttccatttcatatgacc-tacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
||| | || | ||| | ||| | || | || ||| || | | | | | || ||||| ||||||||||| | | |||||||| || || ||||||||| |||||| |||||||||||||| ||| |||| ||||| |||||||||||||| |
-------------------------------------------gtaaagcacattcagggagctt--agttgatcc-gcttgctatataga---tttctgagaatccatgtgacgattt----cagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagac-----acttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
||| | ||||| | ||| ||| | | | |||| ||| | | || ||| | | | | ||| || | | | | | || || | | | ||||||||||||||| ||| |||||||||||||||||||| || ||||| || || || ||| |||| || |||||||| || || |||||||| |||||||| |
gtaataagtaacttcttttgtggataggtgcctgtattggcatttgtatttactttttgtgtatttatatatatatatatgtgtgtgtatgtatatatacatacacaatacatatatactttcttatagtgcaacacttcaacttgtgaatagctgcgttggtgacatatcgtctgctacagGTTGATGAGAGGGGCATGCGCTGGTTTTATACTGGTGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTA
upper sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ36404 (Selaginella moellendorffii), 3'ss of exon 8
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
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-----------------------------------------------------------------------gtaagtagctgctcctacgaaactcgttgg---ctaaaattttggatgatcgtagACGGACGAGAATGGCCTGCGATGGTTTTACACGGGCGATATTGGGCAGTTCCACCCGGATGGATGTTTAGAGATAGTCGATCGAAAGAAGGATATCGTTAMapped 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|11274197|gb|BF324565.1|BF324565EST: TGACAGCTGGTTACTTTAAGAATCAAGAAAAAACTAAAGAAGTGTTCAAG GTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTC
genomic: TGACAGCTGGTTACTTTAAGAATCAAGAAAAAACTAAAGAAGTGTTCAAGgtaatttcca ... cttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
ttttaac putative branch site (score: 2)
ttacatttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
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