Sequence
atgc intronic sequence ATGC exonic sequenceAATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag
Basic information
species | Glycine max |
transcript | GLYMA08G12120.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag
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ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaa-gttttgcaatcttattgtttcag--
upper sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 4
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatat-gcaatttattttcttttgatcact-catttaattattatgttctttcttag-----------------------------------------------
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AACGGCAAGCAAATGGTGCAAGAGGGAGCATTGACAGCTTTAGCATCAGTAGCTGATTCATCGCAGgtaatttgtccatgtataagttagcttaatttcttatagggggagggggacgcaacattaccttttatacttatcttgatggttaatgagagtttataatattgtgttaaattttggtgtacttgtcttgcag
upper sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G033619_T01 (Zea mays), 5'ss of exon 3
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag
| ||| || || ||||||||||||| ||| ||||||||||| ||||||| || ||||||||||||||| | ||| | | |||||||| | || || | | || | | | | | | | |||
ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcaggaaataca--gttcaatccttcttgttaacatagtaatctaacataaattttcaatcttatttattcag------
upper sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 4
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaac-atatgcaatttatttt-cttttgatcactcatttaattattatgttctttcttag
|||||||| || |||||||||||||| || ||||||||| | || ||||| |||||||| || ||||||||| | | |||| ||| | | | | | || || |||||| | | | | || || | || |||
AATGGTAAACAAATGGTGCAAGAAGGAGCTTTAACTGCTCTTGCTTCAGTGGCTGATTCATCACAGgtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatc--taagtctaacataatctaaatttgtag
upper sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 4
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag
||||| || || ||||||||||| || ||||| |||||||| || || ||||||||||| ||||||||||| | | || | ||| | | || ||| | | || | ||| || || | |||
AATGGAAAACAAATGGTGCAAGAGGGGGCCTTGACTGCTTTAGCGTCTGTTGCTGATTCATCTCAGgtattatata-------ttttaaaatatgcttccattatggttttcttataaatgagcagcctaacacttttgagtatcaatagMapped 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|20812511|gb|BQ296989.1|BQ296989EST: TGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAG GAACACTTCCAAAAATATTATGATGCTGTAATGCCATACCTGAAGGCTATA
genomic: TGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtg ... tctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag
- - - - - - - - GCAAGA
- - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT