Sequence
atgc intronic sequence ATGC exonic sequence...tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA20G01240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
---tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaa--tttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
| || |||| | | | | ||||||| ||| | || | ||| | | || || | | || | |||| ||| ||||| ||||| || ||||| ||||| |||||||||||||| || || |||||||| |||||||| ||| |||| |||||||||||||| || |||
ctgtgcatgtgtcttgtttagcctttcggggaatttgtg---cctggaatcttttttaactttattctgatcatgtcatgactttt--ttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
| ||||| | | || || || | | | | || ||| | | | | || | | |||||||||| || || || ||||||||||| ||||| || ||||| || || || || |||||||| ||||||||||| ||||| ||||| || || |||
actttctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgtgattgctgcctggataatattgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatctt----gactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
|| | || ||||| | | | || || || || | ||| ||| | || ||| | ||||| | ||| |||| || ||||||| || || || ||||||||||| ||||| ||||| || |||||||| || ||||| ||||||||| || | ||||| ||||| || ||||||
--taaatttcatttgcttacaatacactatactggcattactttaggaca-ttatctggtttactctaataagcaaatgataaaagacaatctt-tttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 4
tttatctgtcctttg---cctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtg-acacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
| |||| || | || | | | || || | |||| ||| || || | | | || || | | || || | || | || |||||| || || ||||| || || || |||||||| || || || |||||||||||||||||||| ||| | || ||||||||||| || || |||
tctatcagtagagtagatactgttatcaggtgcctttaaaaagatgtgggacatttgtcttcaactgttggtctacttatacct---cttttttgcatt-gcagTCATCAGTTCTACACTCGCAGCCGAAATCTACAGTGGGAACTCCTGCATACATTGCTCCTGAGGTTCTTCTGAAGAAGGAATACGATGGAAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
--tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttact-tttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
||| | | | || || |||| || ||| | | | | ||| | | | | ||| | | | || | | | | | | ||||||| ||||| || ||||| || || || || |||||||| || ||||| || ||||| |||||||||||| | || || |||||||| ||||||
ggcttaatgtttacacgatggtagtagaataatgaatatgatc-atagcgttgtcagttt-tcttttaactaaca-ataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 4
tttatctgtcctttgccttt-ggttgattaatttgtaatatct-gtgacacaattaatttgtaat--atctgtgacacaaatcttgactg-tcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
| || ||||||| || || | |||| |||| | || | | || | |||| | | | | ||| | || |||||||| || || ||||| || || || |||||||| || || || || ||||||||||||||||| ||| | || ||||||||||| || || |||
-----ttatctggtgcctttcaaaagaaaaagattggccatctagtgagattcttgtctccttattaaactgttgctctgcttctaactcctttttgcattgcagTCATCAGTTCTACACTCTCAGCCCAAATCTACCGTGGGAACTCCAGCATACATTGCTCCTGAGGTTCTTCTGAAGAAGGAATACGATGGGAAG
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 5
---------tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
|| | || || || |||| | || | | || | || |||| | |||||| | || ||| |||| || || |||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| || |||||||| ||||||||||| |||
ataaaacaattgttttgatgttcatct---gttgctgcccctgcc-tcttcatgctattttttattt-tgatatctatatatttaactttggctgtttttct----cagTCCTCAGTGCTGCATTCACAACCAAAATCGACTGTTGGAACCCCTGCATACATTGCTCCTGAAGTCTTACTTAAGAAAGAATATGACGGGAAGMapped 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|18041406|gb|BM309700.1|BM309700EST: ATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGGATTCGAAG GCCTCTGTGCTACATTCACCACCTAAATCTACTGTTGGGACCCCTGCATAC
genomic: ATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCGAAGgtacactttc ... acttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacaattaatttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
gtcttac putative branch site (score: 3)
tcttactttt CT-rich tract
attaatttgtaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttacttttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - ctttgcc
- - - - - - - - - - - - - - - - - - - - - -tgacaca