Sequence
atgc intronic sequence ATGC exonic sequence...tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
Basic information
species | Glycine max |
transcript | GLYMA06G02120.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g04100.2 (Oryza sativa), 3'ss of exon 8
-----tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG------------------------------------------------------------
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cctgtttattgcattgttaaatgtgtgcaccgctcgt--agtgtgacttatgacttatct---gatttccaattgccatccacttatctgatttgatactttcagGATGGTCAAGAACTTGGGGAGAAGAGCATTTTGGTAATGGGTATGTTCCATCATGACGCTGGTCTCGCATTTGGTTTGACTGACACTTGACATTAATAAA
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g04100.1 (Oryza sativa), 3'ss of exon 8
-----tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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cctgtttattgcattgttaaatgtgtgcaccgctcgt--agtgtgacttatgacttatct---gatttccaattgccatccacttatctgatttgatactttcagGATGGTCAAGAACTTGGGGAGAAGAGCATTTTGGTAATGG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 8
-----tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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tgtgatggcgctgaacccagtactttatgacagagatatgaagcagcttttgcttgg----aatattatgtaggctgatacttcacttgtgttgaaactt-tcagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGTAACGG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G110345_T01 (Zea mays), 3'ss of exon 8
tgctaa--catagttatctgtctcgaatatatatt-tggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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tgctggaccccactactttatgatggagatataaagcagtatcatcttttgcttggaataatatgtaggctgataacttcgct-cgtgttgaaacttt--cagGTTGGTCAAGAACCTGGGGAGAAGAACACTTTGGTAACGG
upper sequence: GLYMA06G02120.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G42430.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
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gtcagttccttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctttaaattcctttgtttgactatgtttgtaatctcgcctaacccgataacctcacgtttt--cagGTTGGTCAAGAACGTGGGGAGAGGAACACTTTGGAAACGGMapped 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|151409651|gb|EV279459.1|EV279459EST: CATAGGTTCAAGACATGGAGAAACATGGCACGTATCTCCAAGCAGTGAAC GTTGGTCAAGAACTTGGGGGAGAAGAACACTTTGGAAATGG
genomic: CATAGGTTCAAGACATGGAGAAACATGGCACGTATCTCCAAGCAGTGAACgtatgttgta ... tttttaccagGTTGGTCAAGAACTTGGGG-AGAAGAACACTTTGGAAATGG
EST:
gi|208189656|gb|GD992264.1|GD992264EST: CATAGGTTCAAGACATGGAGAAACATGGCACGTATCTCCAAGCAGTGAAC GTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGGGAAAGTCC
genomic: CATAGGTTCAAGACATGGAGAAACATGGCACGTATCTCCAAGCAGTGAACgtatgttgta ... tttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGGGAAAGTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
tcttaat putative branch site (score: 3)
tttttacc CT-rich tract
ttctaagaaaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctaacatagttatctgtctcgaatatatatttggtttgcttttttttttgttctaagaaaaaaaaatttgatgccacaatgttcttaatttttaccagGTTGGTCAAGAACTTGGGGAGAAGAACACTTTGGAAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
tgctaac
- - - - - - - -ctgtctc
- - - - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccaca