Sequence
atgc intronic sequence ATGC exonic sequence...gtcttccagattcttatttcagtgtaattatcaaattgtaagttgtaagtctagattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
Basic information
species | Glycine max |
transcript | GLYMA08G19260.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 7
---gtcttccagattcttatttcagtgtaattatcaaattgtaagttgtaagtctagattg-attaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
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tttatatgggagattgttttgctagtcacatctccagatccta---tctaaatcacaatggtgttgaatatgaaaaatt-aaccagatccaatgatctctatagGTTGGTTCAATTGAGGGGCGGGTTGGTGTTCATCATCTGGATGATTCTCAACAGAGCAAAAACTTCACATTCAAATGCCACAGAGATGGAAATGATATAT
upper sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
gtcttccagattctt-atttcagtgtaattatca-aattgtaagttgtaagtcta--gattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
||| || ||| || | | | | | || | | || | || | || | || ||| ||| ||| || |||||| || | | | ||| |||| || || ||||| ||||||||||| || |||||| | |||||| || || |||||||||| |||||||||||||| || || |||||||| ||||
-tctcacatattttttactatattttccttttaacaaatttactctttagatttatggatcaatttattaaga-tagttgaatctatctttttgttcttt--agGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
upper sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 6
gtcttccagattcttatttcagtgtaattatca-aattgtaagttgtaagtctagattgattaatttt----gagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
| || |||||| |||| || || | || | | | ||| ||| ||| | | || || |||||| | || | ||| |||| || ||||| || ||||| ||||| || || ||| |||||||| || || |||||||||| ||||||||||| ||| ||||||| ||||| ||||
-----cacaatctttattttttaaaaatttccatggatgaatgtgtttggatggaagtgaataaatttattaggagttttcaatctgatggtttattctttccagGTTGGTTCAATTGAGGGAAGAGTTGGCGTACACCATCTGGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGTCATCGAGAGGGAAATGAGATAT
upper sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------gtcttccagattcttatttcagtgtaattatcaaattgtaagttgtaagtctagattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
|| || |||| || |||| || | | | | ||| | |||| | | | | | || | ||| || | | | |||||||| || ||||| || ||||| || | || || || | |||||| |||||| || |||||||||||||||||||||||||| ||| || ||||
gtgagtcgattcttagtaacggagaaatctcaacaatttgttgtcaagatcgttgtttcgaagtggatgtaacagtgtgaaatgtaccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATATMapped 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|151399353|gb|EV269224.1|EV269224EST: AGTATCAAACAAGGTGCCTTGCTGCATTCCCTGACCAACAAG-TTTCTTG GTCGGATCA-TAGAAG-AAGGGTTGGGGTGCATCATTTGGATGATAGTCAG
genomic: AGTATCAAACAAGGTGCCTTGCTGCATTCCCTGATCAACAAGGTTTCTTGgtatgcatct ... ctttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtctagattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
aactgat putative branch site (score: 3)
tacttttt putative PPT
tagattgattaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttccagattcttatttcagtgtaattatcaaattgtaagttgtaagtctagattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-tcttcca
- - - - - - - - -ttcagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg