Sequence
atgc intronic sequence ATGC exonic sequence...tttctatgtaatagtaattagtgatttaacaagtgtgtttttctccctccttttaaaaccctttcttgatatgtgaattttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
Basic information
species | Glycine max |
transcript | GLYMA20G34520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g10400.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------tttctatgtaatagtaatta--gtgatttaacaag---tgtgtttttctccctccttttaaaaccctttcttga--tatgtgaattttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
|| | || |||| || || | || | | | ||| || | | |||| | | |||| | | | || | | || || | |||||| ||| |||| |||||||||||||||||||| || | || ||||||||||| ||||| || ||| ||| || ||| |||| || || || || ||
gtatgttccatgaaacatttattttctttcttttagtttaatttaacaaggctagtacttcgattcttcataagcattgcgatcatttagtgatctctgtcacatagctggatctttgtattgcattgtggttttgagccaatttcagaaattgcctaaactattgtttgatttttgtgacagCACGGATTTGAGACTGAACCAACCAAGGTATGCAACATTGCCAAACATAATGAAGGCAAAATCAAAAGTCATCAAGAAAGTCACCCCCGAAGATCTGGAT
upper sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008864_T01 (Zea mays), 3'ss of exon 3
------------------------------tttctatgtaatagtaattagt--gatttaacaagt--gtgtttttctccctccttttaaaaccctttcttga---tatgtgaattttgaaccttttcttc-ttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
||| || | || | || || || || | | || | | || | ||| | ||| | | | || | | || |||| |||||||| ||| |||| || ||||| ||||||||||| ||| | || ||||||||||| |||||||| ||| || || ||| | || | || | |
gtagggcccaagaaacatttcaatatattgtttacattttattattcttcgttcgagacgggaaatcgaaatactttgttcagtaatgaataaacttgcgtgaacttgtattaacaattagttttgtctttgctgcagCACGGATTTGAGACTTAACCAGCCAAGGTATGCAACTTTGCCGAACATAATGAAGGCAAAGTCCAAAGTTATTAAGAAAGTTGTCCCTAAAGACCTCGGT
upper sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G43430.3 (Arabidopsis thaliana), 3'ss of exon 4
-tttctatgtaatagtaattagtgatttaacaagtgtgtttttctccctccttttaa-aaccctttcttgatatgtga--attttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
| | || | || | || | || ||| | | ||| | | || ||| ||| || | ||| | | | | | | ||||| |||||| ||||||||||||||||||| ||||| | || || ||||||||||| ||||| || || || ||||| ||| | || | | || ||||
gtgatcactcaa-attattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagctcttga---tgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
upper sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G43430.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------------------tttctatgtaat-------agtaattagtgatttaacaagtgtgtttttctccctccttttaa-aaccctttcttgatatgtga--attttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
||| | ||| || | || | || | || ||| | | ||| | | || ||| ||| || | ||| | | | | | | ||||| |||||| ||||||||||||||||||| ||||| | || || ||||||||||| ||||| || || || ||||| |||
gtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGA---TGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA--------------------
upper sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 4
tttctatgtaatagtaattagtgatttaacaagtgtgtttttctccctccttttaaaaccctttcttgatatgtgaattttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
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cagaaagctgactgcaattatttgccataggctagcataaatgcaacttggctctgtgtttcatctcattacttgacctgatattttgtacctcatgcagCACTGATTTGAGACTGAACCAGCCTCGGTATGCAACACTCCCCAACATTATGAAAGCAAAATCGAAGGTAATAAAGAAGTTCACTCCACAGGAATTGAATMapped 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|151397075|gb|EV266948.1|EV266948EST: GTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAAC CACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAACgtaagtgtca ... cttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
EST:
gi|15814452|gb|BI786727.1|BI786727EST: GTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAAC CACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
genomic: GTTGACGATGGTATTGAAACCGTGTGTCTGAACTTACCAGCAGTAATAACgtaagtgtca ... cttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctccttttaaaaccctttcttgatatgtgaattttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
tcttgat putative branch site (score: 4)
ccttttcttcttgc putative PPT
ttttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctatgtaatagtaattagtgatttaacaagtgtgtttttctccctccttttaaaaccctttcttgatatgtgaattttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- -ctatgta
- - - - - - - - - - - - - - - - gtgtgtt