Sequence
atgc intronic sequence ATGC exonic sequencegtttagcattaatttacatagttcgatttctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
Basic information
species | Glycine max |
transcript | GLYMA05G28650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g63090.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------------gt-ttagcattaatttacatagttcgatttctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
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gtggttttccttcttgatgatctgtttcaatgctctttagccaattttatacgttttctgttatctgctgaaagtattaggagtagactgcat--tttgtcaagtcagagca--ttgcatgacatcactggtctaacttggttttgttcattttcagGGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG
upper sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118586_T01 (Zea mays), 3'ss of exon 6
---------gtttagcat-taatttacatagttcgatttctcttag------taacttgtcagtgatc--attgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
|||| || | || ||||| | | || ||| ||| |||| || | || || || | | || |||| ||||| ||||| || || ||||| |||||||| ||||| |||||||| ||||| |||||||| || || || || || |||||||||||||||
agagctcagctttaccaagttatcaacataactgcttatcccttcagaaatctaaattgttcacgactgaactggtggcaaattatgccttatgttt-cagGGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAG
upper sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14147.2 (Arabidopsis thaliana), 3'ss of exon 7
----------------gtttagcattaatt----tacatagttcgatttctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG----
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gccttggctttagatggtttactgtttattcccctgcattgtgtgaacgatcc-attcccttattcccttcaattggtttc--tttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGGCAA
upper sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------gtttagcattaatt----tacatagttcgatttctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
||||| || ||| | ||| || || || | | ||| | |||| | || ||||| | | | ||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||||| || || || ||||| || ||| | || |||||||||
gccttggctttagatggtttactgtttattcccctgcattgtgtgaacgatcc-attcccttattcccttcaattggtttc--tttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAG
upper sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtttagcattaatttacatagttcgatttctc-ttagtaacttgtcagtgatcattgat-gtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
|| | ||||| ||| | |||| || | || || | | | | | || ||| || | | || |||||| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| |||||||| ||||| |||||||||||||||
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGMapped 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|298169680|gb|HO021040.1|HO021040EST: TGTCCATGAGAGCCGAGGCTTTCCAAGTCCTGAGGAGAAAGCCTGTTCAG GGATATGACATTAGCTTCCTTATA
genomic: TGTCCATGAGAGCCGAGGCTTTCCAAGTCCTGAGGAGAAAGCCTGTTCAGgtttagcatt ... ctgttggcagGGATATGACATTAGCTTCCTTATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
ttgctcct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttagcattaatttacatagttcgatttctcttagtaacttgtcagtgatcattgatgtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC