Sequence
atgc intronic sequence ATGC exonic sequence...aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaacttagcttccttaaatattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA08G21770.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 3'ss of exon 3
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaacttagcttccttaaatattatgaaatctcttgtaatca-----cagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
| | || || ||| | || | | | | | | | | | | || | ||||| || |||| | ||||| | |||||||| |||||||||||||||||||||||||| || ||||||||||| || |||||||| || |||
--gcatggaatcattgtaggttaagagataaggtgagatggggttggagatggaaatga--tggcgttcttaattagtatgtt-ttgcttgtgctttttcttcagGTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAG
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g13000.1 (Oryza sativa), 3'ss of exon 3
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaatt-catgtactaacttagcttccttaaatattatgaaatct---cttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
| || | | | | ||| ||| | || | ||| |||| | || || | || || | | | | | | | || ||||| || ||||||| ||| || || ||||||||||||||||||||| ||||||||||||| || |||
----agaacaaatacatcaatggaattgaagatcgtagcttgctacattgcatgcattacaatacataatttgtatctcttctataccaaacattttatttcagGTCAGGAAGGAGAGGCTTGGGGACAGAATAACAGCTCTTCACCAGATAGTTTCCCCATTTGGCAAG
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g14010.1 (Oryza sativa), 3'ss of exon 3
---aggtaaaat--atgcatgatagttgaaagtgagaaaaacacatgatga----attcatgtactaacttagcttccttaaatattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
||| | || ||| | | | | | | | ||| | | || | | | || || || |||| | | || | | | || |||||||| ||||||| |||||| ||||||||||| || ||||| ||| | || |||||||| || |||
tggcagtagtttccatttggaatatcttggattatgtagtatatatgttaacataatccttacattagg--aggtttcttaggtgtgataatttgtttt-------cagGTGAGGAAGGAGAGGCTAGGGGATAGAATAACTGCACTTCATCAGATTGTATCCCCATTTGGCAAG
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaactt---agcttccttaa-atattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
|| | ||| | || ||| | | | | ||| || | | | || ||| || || || |||| | || |||||||| |||||||||||||| ||| ||||||| ||||| |||||||| || ||||| || ||||||
-ggacagtcatgga--atcattgtggggtggcagagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctc-cagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G072238_T02 (Zea mays), 3'ss of exon 3
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaacttagcttccttaaatattatgaaatctcttgta-atcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
| || |||| || || | | | || ||| || || ||||| | | | | ||| | | ||||| | |||||||| ||||||| || || ||||||||||| |||||||| ||| | |||||||| || ||||||
acttagcatatatatatagtttatgaataacaactacatgcatcacatatcc-tattaactaattgacgtatagtatgagacctgtttttgtacgttgcagGTGAGGAAGGAGAGACTGGGCGATAGAATAACTGCTCTTCATCAGATCGTTTCCCCGTTTGGAAAG
upper sequence: GLYMA08G21770.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 3'ss of exon 3
aggtaaaatatgcatgatagttgaaag-tgagaaaaacacatgatgaattcatgtactaacttagcttccttaaatattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
| | | | | | || || | |||||| | | | | | || ||| || || |||||| ||| | | | | | |||||||||||||||||||| ||||||||||||||||| ||||||||| ||||||||||||| ||||||
aaacagtaaagaaaaaagagagaaattctctagaaaacagaaaactagtaatttaacattctttctttttatatatattaattaatttactctgaac-cagGTGAGAAAGGAGAAGCTGGGTGATAGAATAACAGCCCTTCACCAGTTAGTTTCCCCATTTGGAAAGMapped 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|12496204|gb|BG046947.1|BG046947EST: TTTACAAGAAGACTAAGAGCCAACCATCTTCAAGCCAACCACCTCTCAAG GTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTT
genomic: TTTACAAGAAGACTAAGAGCCAACCATCTTCAAGCCAACCACCTCTCAAGgtgactactc ... gtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTT
EST:
gi|14991661|gb|BI317334.1|BI317334EST: CAACCATCTTCAAGCCAACCACCTCTCAAG GTGAGAAAGGAGAAGTTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTT
genomic: CAACCATCTTCAAGCCAACCACCTCTCAAGgtgactactc ... gtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattcatgtactaacttagcttccttaaatattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
tactaac putative branch site (score: 0)
tctcttgt putative PPT
ttaaatattatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggtaaaatatgcatgatagttgaaagtgagaaaaacacatgatgaattcatgtactaacttagcttccttaaatattatgaaatctcttgtaatcacagGTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - -gcatgat
- - - - - - - - - - - - - - - - - aacacat
- - - - - - - - - - - - - - - - - - - - - - - - -catgtac