Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
Basic information
species | Glycine max |
transcript | GLYMA15G15310.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
--------------------gtttgtttcaaatgtttcatgaacacattattttt--ttctctgtctgacacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
||| | || | | || | | ||| ||| || || | ||| | | || | || ||| ||||||| |||||||||||||||| ||||| |||||||| | ||||| |||||||||||||| ||||||||||| ||||
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattact--atg-cagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
-------------gtttgtttcaaatgtttcatgaacacattatttttttctctgtctg-acacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
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gtatgttgaaacaaatgaattaccatgctttgttcaga-ataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttg-----ctgatttag------------agtatggaatgata----gGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
|| || | | ||| || ||| | |||| | | | ||| || | | ||| | | || | | || ||||||| |||| |||||||| || ||||| ||||| ||| | |||||||||||||| ||||||||||||||||| ||||
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
gtttgtttcaaatgtttcatgaacacattatttttttc-------tctgtctgacacattgttgctgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
|| |||| ||| | ||| || || ||| ||| || | | | | ||| ||| | || ||| | || || |||| || |||| ||||| ||||| ||||| ||||||||| | |||||||| ||||||||||| ||||||||||||||||
gtatgttgcaact-tttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttgc-tgatttag--agtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
|| | | | | | | | |||||| || | | | | ||| || | | || | | | | ||||||||||| || ||||| || || |||||||| ||||| || |||||||||||||||| || || || ||||||||||| |
-gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgt-tgctgatttagagtatgga-atgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
|| |||| | || ||| ||| | ||| || || | | | | |||| | || | | ||||||||||| | ||||| || ||||||||||| ||||| || |||||||||| ||||| ||||| || ||||||||||| |
gtcggttttat---ttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------gtttgtttcaaatgtttcatgaacacattatttttttctc-tgtctgacacattgttgctgat----ttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
| || || || | || | |||| | ||| | | ||| | || | | | || | ||||| || |||||||| || || ||||||||||||||||||||||||||||||||||| || ||||| ||||| ||||| |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------gtttgtttcaaatgtttca---tgaac-acattatttttttctctgtctgacacattgttgctgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
||| | | || || | | ||||| | | | | | ||||| | | |||| | ||| | || | | | |||| || || |||||||| || || |||||||||||||||||||||||||||||||| || ||||| ||||| ||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgt-tgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
| || ||| || ||||| || | | | || | | | ||||| ||||||||||| || || || |||||||||||||| ||||||||||||| |||||||| || || || |||||||
----------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgt-tgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
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--------------------------gttggttgtttt--cgtttgacaagttacatacatgactcttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGMapped 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|23063995|gb|BU578768.1|BU578768EST: TTGTTCCTGTCGATGAGCGCATGAGAGTACTTGATGCAAATGGAAACCTG GTTCCTCATTTGTATTGTATTGGTGATGCA
genomic: TTGTTCCTGTCGATGAGCGCATGAGAGTACTTGATGCAAATGGAAACCTGgtttgtttca ... ggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatttttttctctgtctgacacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
tgctgat putative branch site (score: 3)
ttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA