Sequence
atgc intronic sequence ATGC exonic sequenceAATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga...
Basic information
species | Glycine max |
transcript | GLYMA13G36940.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 4
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacga-taaatttttaatgcat-----------agatgcagttaacactgt-----ggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga-----------------------
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TATTGAAGCCAAACAGGTTGCTGCACAAGAAGCTGAGCGTGCTAAGTTCATTGTTGAGAAAGCTGAGCAAGACAAGAGGAGTGCGATTATCAGGGCACAGgtaagaaatctgttttatagccattgcctgatgtcatgtgccggagatacagtttgacagtacatattatataatggttttgccattgcatgtctagttaacattgtctcttaaacatggcctttctcttctttcaacag
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 4
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtga---------cgataaatt-tttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga---------------------------------------------------------------------------------
||||||||| |||||||| ||||||||||||||||| | || || || |||| || || ||||| ||||||||||| ||||| | || ||||||||||| | | || ||| ||| | |||||| | | ||| | | ||| || | || || || | |||| | ||| || |
AATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCAAAGTTCATTGTTGAGAAGGCTGAACAAGACAAGAGGAGTGCGATCATCAGAGCACAGgtaagcaaagatgcaatggattatttctggtttagatg--gctttcaccatattccttgataagtttactacctgtagttttagtgacaattgttaagacatatcaatggcactgtttatttcttcattgtttcatatatttcatttttgttggtgtgggttgagtctgactgtgaggcctgcttgaacag
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 5'ss of exon 4
------------------------------------------------------------------------------------AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAA-TTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga
||||||||| |||||||| ||||||||||||||||| | || ||| || |||| || || ||||| ||||||||||| ||||| | || ||||||||||| | | | ||
GACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAGAGTTCACCCATGCAATTGAAGCCAAGCAGgttgctgcacaagaagctgagcgtgcaaaagttcattgttgagaaggctgaacaagacaagaggagtgcgatcatcagagcacaggtaagcaaagatgca-------------------------------------------------------------------------------------
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G145964_T01 (Zea mays), 5'ss of exon 1
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgata--------aatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaatt--ttatatttccaatacagtatgtgtattaagga
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CATTGAAGCGAAGCAGGTTGCGGCACAGGAAGCTGAGCGTGCTAAGTTCATTGTCGAGAAAGCTGAACAAGATAAGAGAAGTGCAATTATCAGGGCTCAGgtaaggaaccagttcatgattttggttgcatcatcataagatgtattgctgagttagctctagtgcccttgtgatttatttttttttcaattcgtcttgt----------
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: AC217358.3_FGT005 (Zea mays), 5'ss of exon 4
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgt-gacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtt--tcttctaattttatatttccaatacagtatgtgtattaagga
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CATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCCAAGTTCATTGTTGAGAAGGCTGAGCAGGACAAGCGCAGTGCAGTTATCAGGGCACAGgttagtggccaccctttcttgtgtaagagtgttc--ttttgtctggctggaaacaagtaaaacttacaaggaaaaaaaagaaatgccatgactttaatcgtg-
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G352289_T02 (Zea mays), 5'ss of exon 3
AATTGAAGCAAAGCAGGTAGCTGCACAAGAA----GCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacga--taaatttttaatgcatagatgcagttaacactgtggt-gcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga
||||| |||||||| |||||||||||| ||||| | ||||| ||| |||| || |||||||||||||| ||||||||||| | ||||| || ||||| | | | || | || | | | | |||| || | || | | || | | | || || || ||
----GAAGCCAAGCAGGTTGCTGCACAAGAAGCAAGCTGAGCGTGCTAAGTTTATTGTTGAGAAAGCTGAGCAAGATAAGAGAAGTGCAATTATTAGGGCTCAGgtaagaaaccggctcactattaagtaattatttcaatgattttggttgcatcataaggtctattgctgagtgccctcatgttattttcaatttgccttgt---
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G352289_T01 (Zea mays), 5'ss of exon 3
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGC----TGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacga--taaatttttaatgcatagatgcagttaacactgtggt-gcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga-
| |||||||| |||||||||||||| ||| | ||||| ||| |||| || |||||||||||||| ||||||||||| | ||||| || ||||| | | | || | || | | | | |||| || | || | | || | | | || || || || | |
--------CCAAGCAGGTTGCTGCACAAGAAGCAAGCTGAGCGTGCTAAGTTTATTGTTGAGAAAGCTGAGCAAGATAAGAGAAGTGCAATTATTAGGGCTCAGGTAAgaaaccggctcactattaagtaattatttcaatgattttggttgcatcataaggtctattgctgagtgccctcatgttattttcaatttgccttgtgaag
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 5
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga
||||||||||||||||| || || ||||| ||||| ||||||| || |||| || || || || |||||||||||||||||||| || | || ||||| | || | | | || | || | | | ||| || || | | || || | | | ||| | | | ||||||
CATTGAAGCAAAGCAGGTGGCGGCTCAAGAGGCTGAGCGGGCTAAGTTCATTGTTGAGAAGGCCGAACAAGACAAGAGAAGTGCTGTTATCCGCGCCCAGgtaaagagattctctacatttccacttgtaatctaaactctg------agagcgaaattgttgtgtgacgaaagttc--acatggcttgtgtag------
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 6
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgctta-gtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga----------------------------------
|| |||| ||||||||| ||||| ||||| || || ||||||| || |||| || |||||||| || ||||||||||||||||| || | || ||||| | | ||| | | ||| || | | || | || || ||| || | | |||| ||| | | | | |||| |
CATAGAAGGAAAGCAGGTCGCTGCTCAAGAGGCCGAACGGGCTAAGTTCATTGTCGAGAAAGCTGAACAGGACAAGAGAAGTGCTGTTATCCGCGCCGAGgtgtgaaaagtgtttctctcttttctagcattttaaaaaccggagattgtgttaaagcttgcttttttttttcttttttgttgtg--aactattttaaagcttgctaactgatgtttctgcatgggtttatgtag
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagttt---cttctaattttatatttccaatacagtatgtgtattaagga
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TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat---
upper sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 6
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga-
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TATTGAGGCTAAACAAGTGGCTGCACAAGAAGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaatggtccatccataccctaagaaatgcaaatctttgtttccatttaagctgctgcagtgttctgaac-taggattttctgcaaccatMapped 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|192307654|gb|FG999693.1|FG999693EST: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAG GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataa ... aatctttaagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagtttcttctaattttatatttccaatacagtatgtgtattaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA