Sequence
atgc intronic sequence ATGC exonic sequenceCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg...
Basic information
species | Glycine max |
transcript | GLYMA01G12340.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgtttgaatggtgaatc-tgtttgttgattttttatgtgcggaaatttgtatcggtttgca-atatgattgtgtggctg-----
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-----CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacc--cccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgatttt-gtttgaatggtgaatctgtttgtt----gatt--ttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg
| |||||||| |||||||| |||||||| || || |||||||||||||||| ||||| ||||| ||||| || |||||||| ||| || |||||| ||| | | | | | |||| || ||| | | || | | || | | | | | || | || | | ||
-----CCAAGAACCCGACCTGGGCCTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCTGCCGTCCACCGTAGCCTCGGCGTTCACGTCTCCTTCGTCAGgttccccctcatacacccccgcactccttctatgtctgcctgccttacaattcatatcatttactgaggtgcct-tgagctaatcatgtatttttttctct-
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgt----ttgaatggtgaatctgtttgttgattttttatgtgcggaaattt--gtatcggtttgcaatatgattgtgtggctg
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-----CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctcccgttccagatctcgccatccctccgccccg-
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggca--agtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatg-tgcggaaatttgtatcg-gtttgcaatatg-attgtgtggctg
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-----CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGGTCCACATCACCTTCGTCAGgtaccaaccactactactccctctcgacttgcacaatcgcgtatcagatcttgctgcttccgctccagatctcacgctcccgacttgcacaatgagggca
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G134045_T02 (Zea mays), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgagg----caagtttttgctgattttgtttgaatggtgaatctgtttgt----tgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg
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-----CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGTGTCTTCCTCTGCATCGACTGCTCGGCGGTGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgcctcgcctcacctcacctcacctgcttccctttccttctcacacttgtccatgtacgtggaactgtggccatgcccccggtgcatg-atagt--
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G094390_T01 (Zea mays), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgagg----caagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgat-tgtgtggctg-
| |||||||| || |||||||||||||| || || |||||||||||||||| ||||| || | |||||||| |||||||| ||| || |||||| ||| | | | ||| || | || | | |||| | | | || || || || | ||| | ||| | | |||
-----CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgcctcacctgcttctcttctcttctcacacctgtccacgtacgtgg-acctgtggccatgcctaaatgcttgtagtatactgtactaatctgc
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: AT2G35210.2 (Arabidopsis thaliana), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtt------tttgctgatttt--------gtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg------------------
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-----CGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCGTCCACATTAGCTTCGTCAGgtcatttgattcattcattcattttcatcttctgattctattatagagacatttcctaataatctagggtttagagaatctgctttttagccaagaaattgtgttgatcttcattttttgtttttag
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: AT5G46750.1 (Arabidopsis thaliana), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttg-----tttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg--
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-----CGAAGAATCCAACATGGGCTTCTGTTCCTTATGGGATCTTCCTATGCATCGATTGTTCTGCTGTTCATCGAAGTCTAGGTGTTCATATCAGCTTCGTCAGgtaaaactttg--aatcttgaggaacacaaatttgaactctttaggcttaatttttagcttcatggacttgtagcaatgtttcaccttctggctagggttta
upper sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 2
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagttt--ttgctgattttg----tttgaatggtgaatctgtttgttgattttttatgtgcggaaatttg---tatcggtttgcaatatgattgtgtggctg
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-----CGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaattttgagttttggtggtttgatccatgatttagggttttggcagttca-atttggtgatttgatatttcgactagggttttgatt-taagat--Mapped 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: GCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTC GTGAG
genomic: GCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaag ... atttcactagGTGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgtttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctg
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