Sequence
atgc intronic sequence ATGC exonic sequenceCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct...
Basic information
species | Glycine max |
transcript | GLYMA01G12340.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtgaatc-tgtttgttgattttttatgtgcggaaatttgtatcggtttgca-atatgattgtgtggctgattct
| |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||| |||||||| |||||||| ||||||| |||||| ||| ||| | | || || || | | | | | | | | ||| | | || || |||| | || || |
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacc--cccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgat-tttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggt-ttgcaatatgattgtgtggctgattct--
| |||||||| |||||||| |||||||| || || |||||||||||||||| ||||| ||||| ||||| || |||||||| ||| || |||||| || ||| || || | | | ||| || || | | |||| ||| | | || ||| | ||||
CCAAGAACCCGACCTGGGCCTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCTGCCGTCCACCGTAGCCTCGGCGTTCACGTCTCCTTCGT----CAGgttccccctcatacacccccgcactccttctatgtctgcctgccttacaattcatatcatttactgaggtgccttgagctaatcatgtatttttttctct
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgt----ttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct
| |||||||| |||||||| |||||||| || || |||||||||||| |||| |||||||||| |||||||| ||||| || ||||||| |||||| ||| | | || | || | | | | || | | | | | | | | | | ||| || | | | | |
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctc----ccgttccagatctcgccatccctccgccccg
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgca--agtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatg-tgcggaaatttgtatcg-gtttgcaatatg-attgtgtggctgattct
| |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||| ||||| |||||||| || || || ||||||| |||||| ||| | | | || | | || | | | | | | | || || | | | | || | | | | || | || ||
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGGTCCACATCACCTTCGTCAGgtaccaaccactactactccctctcgacttgcacaatcgcgtatcagatcttgctgcttccgctccagatctcacgctcccgacttgcacaatgagggca-----
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G134045_T02 (Zea mays), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttg-caatatgattgtgtggctgattct
| |||||||| || |||||||||||||| || || |||||||||||||||| ||||| || || |||||||| |||||||| ||| || |||||| ||| | | | | | | | | | | | || | | || | || | || | ||| |||| |
CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGTGTCTTCCTCTGCATCGACTGCTCGGCGGTGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgcctcgcctcacctcacctcacctgcttccctttccttctcacacttgtccatgtacgtggaactgtggccatgcccccg-gtgcatgatagt
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G094390_T01 (Zea mays), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGg----caagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct-
| |||||||| || |||||||||||||| || || |||||||||||||||| ||||| || | |||||||| |||||||| ||| || |||||| ||| | | | ||| || | || | | |||| | | | || || || || | ||| | ||| | ||| || ||
CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgcctcacctgcttctcttctcttctcacacctgtccacgtacgtgg-acctgtggccatgcctaaatgcttgtagtat-actgta---ctaatctgc
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G35210.2 (Arabidopsis thaliana), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtt------tttgctgatttt--------gtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct-------------
|||||||||| || ||||| ||||| || || |||||||| ||||||||||||||||| || ||||| || ||||| ||||| ||||| |||||||| ||| | || || | ||||| | || || | | ||| | || | || | | | | || || | ||||||| | | | |
CGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCGTCCACATTAGCTTCGTCAGgtcatttgattcattcattcattttcatcttctgattctattatagagacatttcctaataatctagggtttagagaatctgctttttagccaagaaattgtgttgatcttcattttttgtttttag
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G46750.1 (Arabidopsis thaliana), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttg-----tttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattg-tgtggctgattct
||||||| || || ||||| || || | |||||||||||||| ||||||||||| || || ||||| || ||||| || || || ||||||||||| ||| || |||| || ||| ||| | ||| | | | | |||||| | | | ||||| | | | | | | | | || | |
CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttg--aatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta----
upper sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 2
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtg-aatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct----
|||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||| || | ||||| || || |||||||||||||| ||| | ||| | || |||| |||| ||| | || |||| | || || || || | | || | | |||||
CGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtga-tttcaatt--ttgagttttggtggtttgatccatgatttagggttttggcagttcaatttggtg--atttgatatttcgactagggttttgatttaagatMapped 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|7146935|gb|AW508857.1|AW508857EST: GATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAG GTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACGATGAGCTT
genomic: GATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagttttt ... ctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACGATGAGCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct
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