Sequence
atgc intronic sequence ATGC exonic sequence...tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
Basic information
species | Glycine max |
transcript | GLYMA18G19670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g50260.1 (Oryza sativa), 3'ss of exon 3
-------tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
|| || | ||| | | | || | | | | | || ||| | || ||||| | || || | || | || ||||| ||||| ||| |||| || || || || ||| ||||| | |||| ||||| |||||||||||||||||||| ||||||||||| |||||||||
ttcagtgctcacttgtagaaaccgacaggattcaggac-taagggaaagctaaaaacac---tagtacaagtatctgaagtaatatttgctctctgtgat---gcagGCGATGATTGTGTTTCCATCCAGACAGGCTGCAGTGACATAAACATACATAATGTGAACTGTGGACCAGGGCATGGGATCAGCATTGGTGGTCTAGGAAG
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
tgcaaatggacaaaaaattaaagta-aaacacatgatgtagacttact-gacataaatggtccaagttggctca-atatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
||| | | | | || || || || | | | ||||| ||| || | || | | | | || || || || | ||| |||||| |||||||| | || || ||||| |||||| || ||| || |||||||||| || |||||||| || |||||||||||||||||| | |||||
---aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtaatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
tgcaaatggacaaaaaattaaagta-aaacacatgatgtagacttact-gacataaatggtccaagttggctca-atatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
||| | | | | || || || || | | | ||||| ||| || | || | | | | || ||||| || ||| |||||| |||||||| | || || ||||| |||||| || ||| || |||||||||| || |||||||| || |||||||||||||||||| | |||||
---aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtattttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 5
--tgcaaatggacaaaaaattaaagtaaaacacatgatgtagact-tactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
|| ||| | | | || | ||| | ||||| | || || | || | || || || | | | | | ||||| ||||| || || || || || || |||||| |||||| || ||||||| || || ||||||||||| |||||||||||||| || | |||||
cctgtaaaccctgcatgtcaaaggacatgtttcagagttaagagtacactgaaa-aactgctgtaaactagcataacattcctttgtcctattcgat--gcagGTGATGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACACAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgc-agGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
| | || || | | | |||| | | || | ||| | ||||| | || || ||||| || | || | | |||| | |||||| || ||||||||||| ||||| || ||||| || | ||||| |||||||| || ||||||||||||||||||||||||||||| || || || ||
---gtacgaactaattgtaatcgaaaaaatcgttata-aaact------cgtaaata--tcgggt---cttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G10640.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
||| | | || | | | | |||| || | || || || || | ||| | | ||| |||||||||||||||||| ||||| ||||| || ||||||||| | | ||| |||||||| ||||||||||| || || || ||||||||||| ||||| || ||
-----------------gtaatatgatctccaatcttaaatcctgaatctttaaaaaatctcaatt--cttaa-atctagaaaccttga--attatgcagGAGATGACTGTATCTCGATCCAAACGGGTTGCTCGAACGTGTTTGTGCACAATGTGAACTGTGGACCGGGTCACGGGATCAGCATTGGTAGTCTCGGCAA
upper sequence: GLYMA18G19670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0127g00400.t01 (Vitis vinifera), 3'ss of exon 6
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagactta-ctgacataaatggtccaagttggctcaatata---tttaaatttcaattatt-ttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
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---taacacataagcatagctaatagcccagacaattaacatctaacaggcccatatg--tagatatattctaatacgggctctaaatcttaatgctcactgcagGAGATGACTGTGTTTCTATACAAACTGGATGCTCAAATGTATACATACACAATGTGAACTGTGGGCCAGGACATGGGATCAGTATAGGAGGACTTGGAAGMapped 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|193438891|gb|FK410358.1|FK410358EST: CCTTCAGAACTCCAAAGATGTGTTGATATACAGCAGCTCTATGGCCTGCG GAGATGACTGTATTTCGATACAAACTGGNTGCTCGAACATATATGTACACA
genomic: CCTTCAGAACTCCAAAGATGTGTTGATATACAGCAGCTCTATGGCCTGCGgtaagttatg ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACA
EST:
gi|208088988|gb|GD887817.1|GD887817EST: CAGAACTTCCTAAAGTATTGTGTTGATATACAGCAGCTCTATGGCCTGCG GAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACA
genomic: CAGAAC-TCC-AAAG-A-TGTGTTGATATACAGCAGCTCTATGGCCTGCGgtaagttatg ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
ttatttt CT-rich tract
tcaatatatttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatatatttaaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACATATATGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -aaaaaat
- - - - - - - - - - - - - aacacat
- - - - - - - - - - - - - - - - - - - - - -tactgac