Sequence
atgc intronic sequence ATGC exonic sequence...agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
Basic information
species | Glycine max |
transcript | GLYMA02G09680.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g02210.1 (Oryza sativa), 3'ss of exon 2
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtga-agGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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---------gtaagacggacgattcaact-gtgttcgtcttggatttcaagcgagattcagtaa------aaaattcagaaaacattcatctccgtttcagGTACCTGGAGAACAGCGGCTGCGTCGGAATGTGCGTCAACATGTGCAAAATTCCGACGCAAAACTTCTTCACCAACGAGTTCGGACTCCCTCTCACCATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 1
--agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
| | ||| | | ||| | ||| | | || || | | | | | ||| | || || | | | ||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||| ||||| || || | || |||
gtaacaagtgaattccatcaaaatgactatt---actagtt---gtcttgttcaaaatgtgacagacttgctcctactg--ttgat-----------tgaagGTATCTGGAGAACAGTGGGTGTGTAGGAATGTGTGTGAATATGTGCAAGATTCCAACCCAAGATTTCTTCACCAATGAGTTTGGCCTCCCACTCACCATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 3
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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catatgtcacagtaaccaaatttcaatatattagaaataaaataatgtccaactactaatctttcttttttttctttttctgacaaattctcctatcaagGTACCTGGAGAACAGTGGGTGTGTGGGAATGTGCGTGAATATGTGCAAAATTCCTACTCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S6_190V6.1 (Physcomitrella patens), 3'ss of exon 4
--agctagtatttattttgaaatttacttct----tgcattaattaaggccgttgtaacaatt-tcaccatttttccattgtttccttgatatttattcttgtgaa--gGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
| | |||| ||| | || || | | ||| | | ||| | | | | | | | ||| | || ||| | ||||| || |||||||| || || || ||||| |||||||||||||| || || ||||| ||||| ||||| |||||||| || ||||| | || |||
gtacttgccatttttttccactcttgttttccctctattctgcttatcttgaatctgtcaagtgttgtagaggtggtactaatgacacaatagctgcggatgagaacagATACCTAGAAAATAGTGGATGCGTCGGGATGTGCGTCAATATGTGCAAAATCCCGACCCAGGATTTCTTCACCAATGAATTCGGTCTTCCACTTACTATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23359 (Selaginella moellendorffii), 3'ss of exon 4
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtgagatttctacaaagaagaga--actaagcatgtaaaaatacgtttccagGTATCTAGAGAACAGCAACTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 4
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtgagatttctacaaagaagagaactaagcatgtaaaactacgtttcc--agGTATCTAGAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23185 (Selaginella moellendorffii), 3'ss of exon 3
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccat-tgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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------------------------------------------------gtaagaattctacaaagaagaaaagtgcgcatgtaaaaattgcttttcc--agGTATTTAGAGAACAGCTCCTGTGCTGGAATGTGCGTAAATGTGTGTAAAATTCCCACCCAAGATTTATTCACAAATGACTTTGGACTGCCTCTGACCATG
upper sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25185 (Selaginella moellendorffii), 3'ss of exon 3
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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---------------------------------gtaagaaatctacaaagaagaaaactacgcatgtaaaaatgtgtt-ttgcttttgatttcc----agGTATTTAGAGAACAGCTCCTGTGCTGGAATGTGCGTAAATGTGTGTAAAATTCCCACCCAAGATTTATTCACAAATGACTTTGGACTGCCTCTGACCATGMapped 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|13478196|gb|BG507770.1|BG507770EST: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAG GTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
genomic: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttca ... tcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
EST:
gi|51336380|gb|CO980246.1|CO980246EST: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAG GTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
genomic: GAGATAAATGGAGTGAAGCAAAAAAGTGGCGTGCATATAAAGAAGTGCAGgtagatttca ... tcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
tttattctt CT-rich tract
ttgatatttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctagtatttattttgaaatttacttcttgcattaattaaggccgttgtaacaatttcaccatttttccattgtttccttgatatttattcttgtgaagGTACCTGGAGAATAGTGGCTGTGTTGGAATGTGTGTCAATATGTGCAAGATTCCTACCCAAGATTTTTTCACTAATGAATTTGGACTTCCGTTAACAATG
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