Sequence
atgc intronic sequence ATGC exonic sequencegttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
Basic information
species | Glycine max |
transcript | GLYMA18G43720.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G177654_T01 (Zea mays), 3'ss of exon 1
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgttt-agGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
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------------------------------ctacgtttctttgtactatggttctgttgaagcccattcacg-----------gtaaactagttttctgcgcaaagaacccttttatgatggctggataatgttctttcagGTTAGGCTGGATCCTTCTAGGCCCTTGAGCAGACACAAGCACTGGGTTGTTGCTGAAATTCTCCGCAGAGCTAAGGTGTACGTTCCACCAGCTGCAACAG
upper sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G108008_T01 (Zea mays), 3'ss of exon 1
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
| | | || | ||| | |||| || | |||| | | | || | |||| | | | | ||| | ||| | | || | || ||||| | ||||| ||||||||||| ||||||| |||| |||||||||||||||||||||||| | || || |||||||||||| | | |||
---------------------------ctagcgttcctttga--actaaggttctgttgaagtccattcacgataaattagttttcctctcagaactcttttta---tgatggctgtat-actgttct-------ttcagGTTAGGCTGGACCCTTCTAGGCCCTTGAGCAGATATAAGCACTGGGTTGTTGCTGAAATTCTTCGCAGAGCTAAGGTATATGTTCCACCAGCTGCAACAG
upper sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
----------gttagtagcatgaacttacaattttatttggtttattcttcatcactt----aaattcttgtgcatgtt--attcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatg-ttgttt--------agGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
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gtattttccccttcattttttgaatttgatatac-atttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
upper sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCAC-TGTCCACGCCAG
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--------------------------------------gtcagttgttaaagcaatcggttccttcctttctccactt---ctgctttttcataatgg---ataaaataacttgtgaaacaacattatcat----tccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG-
upper sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0070g00100.t01 (Vitis vinifera), 3'ss of exon 2
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCAC-TGTCCACGCCAG
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--------------------------------------gtcagttgttaaagcaatgggttccttcctttctccacttccgttttttcataa----tggataaaa--taacttgtgaaacaacactgtcat----tccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCAGAAATTCTGAAGAAAGCACGAATCTATGTGCCACCTGAACCTATTA-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|12690557|gb|BG156893.1|BG156893EST: CTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAA GTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTT
genomic: CTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAAgttagtagca ... tgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTT
EST:
gi|12690558|gb|BG156894.1|BG156894EST: CTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAA GTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTT
genomic: CTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAAgttagtagca ... tgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
aaaagttaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttagGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG