Sequence
atgc intronic sequence ATGC exonic sequenceCGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttcttttcctaagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaatgtgatttttttttgccaaagtatgcatgtggt...
Basic information
species | Glycine max |
transcript | GLYMA06G43050.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 5'ss of exon 6
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttcttttcctaagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaat-gtgattttt-ttttgccaaagtatgcatgtggt
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AGGGTTGATACTGCCCTTAAGAACATTGGCATAAACGAGCGAGTGCCCTATAATGCTCCTCTTATTCAATTTTCTTCTTGGATGGGTGGAGACCGTGATGgtatgttacatct----atcatatcatgtttgcaa-----catagttaa------ttaattgtgaaattatggttttaatattgatgtggactacag-----
upper sequence: GLYMA06G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 4
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttcttttcctaagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaatgtgatttttttttgccaaagtatgcatgtggt
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CGTCTGGACACTGCCTTGAAGAACATCGGAATTGATGAGCGTGTTCCTTATAATGCACCTCTCATTCAGTTCTCTTCTTGGATGGGAGGAGACCGTGATGgtat--------------gcaaaggatggcttttgac--ttctgtatagttcagttcttgtgc---atttaataattttgtgc-attgcaccaatttag-
upper sequence: GLYMA06G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 5'ss of exon 4
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttcttttcc--taagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaatgtgatttttttttgccaaagtatgcatgtggt---------------------------------------------------------
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CGTGTGGATACTGCATTGAAGAACATCGGTATCGACGAGCGTGTTCCTTACAATGCTCCTCTTATTCAGTTCTCGTCTTGGATGGGAGGAGATCGTGATGgtgagaaacatatctattttgttgttggttcttagcactatgcct-tataaataattaca---gcacaatg-aatcctctttagatgttgtctttaaattactaccacttaggagataccatgtctgtatgcactctaaatttcaaatgacctttacag
upper sequence: GLYMA06G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 4
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtat----cgttctttt---cctaagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaatgtgattt-----ttttttgccaaagt-atgcatgtggt--
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AGGGTTGACACTGCTCTTAAGAACATTGGCATAAATGAGCGGTTGCCATATAATGCCCCTATCATTCAGTTTTCTTCTTGGATGGGTGGTGACCGTGATGgtacatagcattctctctcccttatttggatagtatatttga-tgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacag
upper sequence: GLYMA06G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G473001_T02 (Zea mays), 5'ss of exon 3
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgt-atcgttcttttcctaagcagttaatgagtggaaacgttcctctctaagcagttt----tatttgt-----caaatgtgatttttttttgccaaagt-atgcatgtggt---------------------------------------------------------------------
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CGGGTTGATACTGCATTGAAGAACATTGGGATTAACGAGCGTGTTCCTTACAATGCACCTCTTATTCAATTCTCTTCTTGGATGGGGGGAGATCGTGATGgtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagMapped 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|26045705|gb|CA783206.1|CA783206EST: TAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATG GTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTA
genomic: TAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttct ... tgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGGGTTGACACTGCTCTGAAGAACATTGGCATAAATGAACGTGTTCCATATAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttcttttcctaagcagttaatgagtggaaacgttcctctctaagcagttttatttgtcaaatgtgatttttttttgccaaagtatgcatgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctctc