Sequence
atgc intronic sequence ATGC exonic sequencegtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
Basic information
species | Glycine max |
transcript | GLYMA20G28740.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttt-tttcatatattaattctttttttc-ttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
|| || || | | | | | | |||| | | ||| | | | ||| ||| | |||||||| || | |||||| |||||||| ||||| ||||| || |||||||| ||||||||||| |||||||| || |||||||| |||||||||||||||
gtaggcgctttt-tgctggatagtctgtactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
-------gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttct----------tgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
|| || | | | || | || | | | | | | |||| | | || | | | ||| |||| |||||| || | |||||| ||||| || || || || ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||||||||| |||
gtatggcgtt-gcgtacttctgttggagattgagatgtatgtacgtgtgttggccatttactcccagaccgtggtgcttacattctacaatgaaatcgcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagcaaattaatatttaactttatttttcactttctaatttaa--accatgttttttcatatattaattcttttttt-cttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
|| | | | | || || | || | || | | | || || |||| |||| | | | | |||||||| | |||||||||||| || || || || ||| | || || || ||||||||||||| ||| || |||||||| |||||||||||||||
-gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagcaaatt-aatatttaactttatttttcactttcta---atttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
|| || | ||||||| |||| || ||| || | ||||| ||| |||| | | || | ||||| || | ||||||||||| ||||| ||||||||| |||| ||||| ||||||||||||| ||| || |||||||| |||||||||||||||
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
------gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaat-------------tctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
| | | | || ||| || | | | | | | | | || | |||||| || || | | |||||||| | ||||| || || || |||||||||||| | || || || ||||||||||||| ||| | |||||||| |||||||||||||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
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gttaggacataattctt--gccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAGMapped 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|192297452|gb|FG989861.1|FG989861EST: CATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGG GATGACCTTAGCAAAACTCCAGCCTCAGCACGACA
genomic: CATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaat ... tttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACA
EST:
gi|18040703|gb|BM308997.1|BM308997EST: CATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGG GATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAAT
genomic: CATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaat ... tttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
tattaat putative branch site (score: 2)
ttaattctttttttct CT-rich tract
taatttaaaccatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA