Sequence
atgc intronic sequence ATGC exonic sequencegtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
Basic information
species | Glycine max |
transcript | GLYMA15G15010.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 13
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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----------------------------------gtgagcttcttctacatgtac--atgtaaacattgtccgttaagttgtt--tgaatatattacagcataggttatgaagattgctattgaaatattgcagGTTTATTGACAATTGGCCCCCGTTTTGGTGGTGCAATTGATGATGCTGCCCGGTACTTCAAAGATGCATATGATAGA
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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---------------------------------------gtcagtcaacattttttttcccccacaaaac-----acataagttctctt--taccgtccaacaatctctaa-gaatgttaaacca-taaaacagGTTTATTGACCATTGGTCCCCGATTTGGTGGTGCCATTGATGACGCTGCTCGATACTTCAAAGACGCGTGTGACAGG
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttctga--aacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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-------------------------------------------------gtgaattaacatc-ccaatccatcaactttttaagtgaagtttgctatataataacttatgctgattatt---cttcaaacaaacagGTCTATTAACAATCGGTCCTAGATTTGGTGGTGCCATTGATGATGCAGCACGATACTTCAAGGACGCTTGTGACAGG
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 3'ss of exon 13
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttct----gaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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---------------------gtaaattgtag---caattatgtttcatttttatttagatg---gagggatcatatcttcat--tggaaatgctgtagtgtgggcttttgtgaac--tgattttataatggaaacagGCTTGCTTACAATTGGTCCCCGATTTGGTGGAGCTATTGATGATGCTGCTCGATACTTCAAGGACGCTTATGATAGG
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S35_384V6.1 (Physcomitrella patens), 3'ss of exon 12
gtaaatacaagcctttaatctgtcaatta---ttgatgtagg-catagtatgaatgtgat-aaggtgaccaaaactttgtatgctaataataataatgccataaaaca-gttagtaatgaataatga--gcttctgaaa---cagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG-----------------------
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gtacgaactt-tctttggtccgttaaatcaactttctgaatgtcacgatctaagaatgtcgaaaatggcactgtgttctgatgctgctggagataaccttctaaatgatgttactgattgtcttccactatatcttaaatatcagGACTGCTCACAATTGGCCCCCGATTTGGTGGAGCTATCGATGATGCTGCTCGTTACTTTAAGGAAGCTCATGACAAGGGCTTGACACCTTATGACTTTGT
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaa--taataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG-----------------------
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gtacagtctaaattgcagaagctatgttatgtatgaagctcttg-aaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaat------actagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ31368 (Selaginella moellendorffii), 3'ss of exon 12
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatga-ataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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--------------------------------------------------------------------------------------gttcgtgtgactccttcatttgtatttttacaactatttgcttgtgcagGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAG
upper sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06573 (Selaginella moellendorffii), 3'ss of exon 12
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatga-ataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
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-----------------------------------------------------------------------------------------gttcgtgtgactccatcggtatttttacaactattttcttgtgcagGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAGMapped 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|193588550|gb|FK540466.1|FK540466EST: GGCCGGGAAGGACCTAATTTCCAGTATTGTATCAG GTATGCTTACAGTTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTC
genomic: GGCCGGGAAGGACCTAATTTCCAGTATTGTATCAGgtaaatacaa ... tctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
tgctaat putative branch site (score: 2)
cttct putative PPT
ttagtaatgaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaataataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG