Sequence
atgc intronic sequence ATGC exonic sequence...aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
Basic information
species | Glycine max |
transcript | GLYMA09G33950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 2
--aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatg-tcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
| | | | || | | | | | | | || | ||||| | ||| | | | | | || | ||| || | ||| | | ||| | || || ||||| || ||||||||||| ||||| ||||| || || || |||||||||||||||| ||||| || | | | || || ||| | |
tatgaatctatgatcattactattttaaggaac-atttctatgttccatttttgc--tgatgtattacacaatgtgtgttgatgacctcgtttggaactacagGCCAGCAAAAAGATTGCTGATGCGAAGCTAGCAAAGGATTTCCAAGCAGTTCTGAAAGAATTTCAGAAAGCTCAACGGTTAGCGGTAGAAAGAGAAGCTG
upper sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
| | || | | || | | ||| |||| || ||| || || | ||| | | || || ||||||||||||| |||||||| |||||||||| || ||||| || || || ||||| |||||||| ||||| | | | ||||| || |||||
-----------------gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtg---tttgat-tgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
upper sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G32270.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------aatg-tttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaaga--aaaagtgaccttcaatgtcttggt---tgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
||| || | | | || || | | | | || | | || | | | | || ||| ||| ||||| || ||||| |||||||||||| |||||||| || |||||||| |||||| | || | ||||||||| |||||||| || |||| | || ||| ||| || |||||
gtaagtgtgtgtttctcaataggaataacttagaaagatgtgagatttgttttcatgaaaacatcacattctgtgaaatttatttactattgatggttctcttttatgaattggtatttgctgatgcagCAAAGTAAGAAGATTGCAGATGCTAAACTTGCAAAGGATTTTGAAGCAGCGTTGAAAGAGTTTCAGAAAGCACAGCATATTACAGTTGAAAGAGAAACTT
upper sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
|| | | | |||| | | || || ||| | | | ||| | ||| ||| | || || |||||||| | ||||| ||||||||||| || ||||| || ||||||||||| ||||| ||||||||||||||| | ||||| || ||||| |
-----------------gtg-agtcatttatgataaaggaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
upper sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
------aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
||||| | || | | | | | | | | |||| |||||| | || | |||| || | | | || ||||| | || |||||||| |||||||| || || |||||||||||||| || || || ||||| |||||||||||||| || || |||| || |||||||| |
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatctttt---ttgaggggtgtaa---ttgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGMapped 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|254315437|gb|GR825246.1|GR825246EST: CGGCTAAGCTTAAGCAAGCTAGTGAGATTGATCACAATGTTGAAGTTAAT ACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTT-CAGGCGGTG
genomic: CGGCTAAGCTTAAGCAAGCTAGTGAGATTGATCACAATGTTGAAGTTAATgtaatgcgtt ... gtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
aaagaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- tgtttgt
- - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - tggcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtc