Sequence
atgc intronic sequence ATGC exonic sequence...tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA12G35510.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactg-gatat-gctaacatttttttttatcata----acagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
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---ctgttctgctagtatcattcggtagtgtttttag---ctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 4
--tgcatttaatact----ttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
| |||| || | | ||||||||| || | |||| ||| | | || | | |||| | |||| | | ||| | | ||||||||||| ||||| || || ||||||||||||||||||||||| ||| | || || || |||||||||
tttaaattttatggcaaaatattctctttgaaaaattacattgatt---aaagggtgagcatttgtact--gctgg-tctgctgctaatgatttcaaactgttcagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAATTCTGAAGGGTACAATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 8
--tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatcttt--gactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
|| | | ||| | |||| || | | | | | ||| | | || |||| ||||| || |||||| | | | | |||||||||||||||||||||||| ||||||||||| || || |||||||| | || || ||||||||||||
aacttgttaagaattttattatgttgagttctcgcctgtgatggtttggtgttattatacaactttcggactgtatttgctaatgatat----aaagttgacagACATTTGTAGGAACACCATTTTGGATGGCACCAGAAGTGATTCAGAACTCCGAAGGTTATAATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 8
-tgcatttaat--actttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
| |||| | || | || || | ||| |||||| |||| | | | || | ||| | || || | || |||||| ||||||||||| ||||| ||||||||||| || ||||||||||| |||| || ||||||||||||
atcaatttgaacaacatctcatctttacttctctgctgatggtttgcaattttcactcattcatctgggttgcgtgcgctgatatgtta---aagaatgacagACTTTTGTAGGAACCCCATTTTGGATGGCACCAGAAGTTATTCAGAACTCAGAAGGGTATAATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 8
tgcatttaatactttgtgca-attgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacattttt---ttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
|| || | || || | |||| | | ||| | ||||| |||| | | |||| | ||| | | ||| | || ||||||||||||||||||||||||||||||||| || ||||| ||||||||| |||| |||||||||||||||
-gctaggaac-caatgaacatgtctaaaagttgaatggatcgaatgcctcttact--tcatttcatgatatatatttttacactaatgtgtttaacaatgacagACATTTGTAGGAACACCATTCTGGATGGCTCCAGAGGTAATTCAGAATTCAGAAGGATATAATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------tgcattta-atactttgtgcaattgaaaaatcacttagatttttaaatttttactct---tcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATAC---AGATGGATATAATGAGAAG
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gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------tgcatttaatac-----tttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgac-tggatatgctaacatttttttttatcataa----------cagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATAC---AGATGGATATAATGAGAAG
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gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 7
tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
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---------------------------------gtaagttttaagat----acacct--ttttataaggaagaagctaac----tcggtaacgaaatcagACATTTGTCGGGACACCATTCTGGATGGCACCCGAGGTGATCCAAAATTCAGATGGATATAATGAAAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 7
tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttg-actggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
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-----------------------------------------gtaagtttaagatacacctttttataaggaagaagctaac----tcggtaacgaaatcagACATTTGTCGGGACACCATTCTGGATGGCACCCGAGGTGATCCAAAATTCAGATGGATATAATGAAAAGMapped 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|11688820|gb|BF596496.1|BF596496EST: CAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG ACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACA
genomic: CAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAGgtaaacatat ... atcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACA
EST:
gi|9899540|gb|BE608508.1|BE608508EST: CAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG ACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACA
genomic: CAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAGgtaaacatat ... atcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
tgctaac putative branch site (score: 1)
catttttttttatc CT-rich tract
atatgctaacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcatttaatactttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACAGATGGATATAATGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
tgcattt
- - - - - - tttgtgc
- - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaac