Sequence
atgc intronic sequence ATGC exonic sequencegtacgctacatacttacatttaatggtgaaccataagtaatgaacaaactcattgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
Basic information
species | Glycine max |
transcript | GLYMA10G32350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 3
gtacgctacatacttacatttaatggtgaaccataagtaatgaacaaactcattgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctc-ttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
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-------------------------------------------acaactgttgtggttgttttgattgtaatattctatttgttgtt-tgtgaactccatcaatagtttgttaatatcccgcaatacaattttatgaactccagAATCTCCCTTTGAATTCCGCGCACTGGAGGTTACTTTGGAAGCCATTTGCAGTTTTCTTGGTGCACGCACTACTGAGTTGGAGAGTGCTGCTTACCCAGC
upper sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgctacatacttacatttaatggtgaaccataagta---atgaacaaactcattgattgcatctgttcctcttataa-atctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
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gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgat--cttttgatgcctacataagaactaatgaaccattcactct---tttcacttttggtattgaagtg-tttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC
upper sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtacgctacat-acttacatttaatggtgaac-cataagtaatgaacaaactcattgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
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gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgat---acctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgat-tgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC
upper sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
gtacgctacatacttacatttaatggtgaaccataagtaatgaacaaactcat-tgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
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---------------gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaa-----------gtagagatttttctgtcttt-------cttgaaaattagttttctgaatgatctgtgtcata-aatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGCMapped 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|9820824|gb|BE556334.1|BE556334EST: TAAAGAGTATCTTGGTGGCCAAAATGATGCTGAAGCAGCTGAAGAAGACG AGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTA
genomic: TAAAGAGTATCTTGGTGGCCAAAATGATGCTGAAGCAGCTGAAGAAGACGgtacgctaca ... tgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTA
EST:
gi|192300565|gb|FG991517.1|FG991517EST: GTGTCGTCCCTGCGGACCCGCAGGCAATGGCGGTTGTGAAGAAGAAGACGCAGTCTTCGAGGAGTTGGATTCTGTTTGACGCCACTGGGCAAGGCACGTTGCTCGACATGGACAAATATGCCATCA
genomic: GTGTCGTCCCTGCGGACCCGCAGGCAATGGCGGTTGTGAAGAAGAAGACGCAGTCTTCGAGGAGTTGGATTCTGTTTGACGCCACTGGGCAAGGCACGTTGCTCGACATGGACAAATATGCCATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
atctaaa putative branch site (score: 3)
atctaaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgctacatacttacatttaatggtgaaccataagtaatgaacaaactcattgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT