Sequence
atgc intronic sequence ATGC exonic sequence...taatggtgtttattttgggcttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
Basic information
species | Glycine max |
transcript | GLYMA14G02380.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 6
------taatggtgtttattttgggcttcatttgtttgatatgcagctacatca-tcttcatttattg-gctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
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gtacctcattagtgtttacttctg-cattatttgtaccaatgaca--tatttcagtttttgtatgctgtgatttcgttttaattatttatattacacatt-----cagGCAATTGATCATATCATCAATTCAGCTGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTG
upper sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
--taatggtgtttattttgggcttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaattactcagttttaacctttgt-tgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
||| ||||| || | || |||| ||||| | || | | | | |||| | | || ||| | | | ||| | | |||||||| ||||| || ||||| || || || || || |||||||||||||||||||| ||||| || |||||||||||||| || || |||||||||||||
aacaataatgtttgttattctctatctttgag-aatatg-aatactgtcgaatccgtatgctggcaaacaaatctcttaatt-gcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
upper sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
taatggtgtttattttgggcttcatttgttt---gatatgcagctacatcat--cttcatttattggctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
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----tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttcttt-cagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
upper sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
taatggtgtttattt-tgggc-ttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaatta--ctcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
| | | || || | || || ||| | | || | | || |||| || | || ||| |||| | || | ||||| |||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||| || || ||||| || ||||| || ||||| |||||||
--gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattga--attgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGMapped 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|209727470|gb|BW663731.1|BW663731EST: ATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAG GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
EST:
gi|151398119|gb|EV267997.1|EV267997EST: ATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAG GCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
genomic: ATGGTCTAAGGCCTGTTGTGGAGTTTATGACTTTTAACTTCTCCATGCAGgttggagttt ... tttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcttcatttattggctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
ttttaac putative branch site (score: 2)
cctttgtt CT-rich tract
ttcatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatggtgtttattttgggcttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaattactcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT