Sequence
atgc intronic sequence ATGC exonic sequence...gtggatcaggtatcataaattgaaccttctttaaaattatttttctttttttttgtgtgtagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 7
gtggatcaggtatcataaat-tgaaccttctttaaaattatttttctttttttttgtgtgtagctttggttgagccttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
||| | | | | || || | ||| | | | | | | | | || | | || | | | | ||| |||| | ||||||||| |||||||| || || || |||||||| || |||||||||||||| ||||| ||||||||||| || ||||| ||||||||| || ||||||||||
aaaactcaaatgtgaaatatgtgtaacttttgtggatggagggagtatcatctatctgcccaatgt--atttatcgatattattttattgtattgtgtgcagAGGTGATAACATCTGCTGAGTTCCACCCTACTCACTGTAATACATTGGCTTATAGTAGCTCAAAGGGCTCCATTCGACTTGTTGACCTGAGGCAGTCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
---gtggatcaggtatcataaattg-aacct--tctttaaaattatttttctttttttttgtgtgtagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
| ||| || || | || || || |||||| | ||| | | || | | || ||| | |||| || | || || | || |||| ||||||| || |||| || || || ||||| || |||||||||||| |||| |||||||| ||||||||||| || || || |||| |||| || |||||
attattgat-gtttaagatgacctggaatctgatctttacacttactgtaattcatgtcc-tg-gtaatat--gttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
--gtggatcaggtatcataaattgaaccttctttaaaattatttttctttt-tttttgtgtgtagctttggttgagccttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
| | | | | | | | | | |||| || | | | | | ||| ||||| | ||| || | | | ||| | ||||||||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||| ||||| ||||| || ||||| |||||||| ||||||| |||||
gctttcctttattgttttta-tcacatatccgttaagtttctactggtggcatctctgttgttagct---gctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 7
--gtggatcaggtatcataaattgaaccttctttaaaattatttttctttt-tttttgtgtgtagctttggttgagccttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
| | | | | | | | |||||| | || | | | | ||||| ||||| | | ||| || | | ||| | ||||||||| |||||||| || ||||| || ||||| || || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| |||| || |||||
gctttcctttattgttttta-tcacatattctttgagtttctactggtggcatctttgttgttagctactgat-agctatggttttgttc--tatcacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACCCACTGCAATACGTTGGCATATAGTAGCTCTAAGGGATCCATTCGACTTGTTGATCTGCGCCAATCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 7
gtggatca--ggtatcataaattgaaccttctttaaaat-tatt--tttctttttttttgtgtg-tagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
| |||| | ||| ||| || | || | || |||| | || || |||| | | || | | || | | ||| ||||||| || || | || || || || || || || ||||||||| | |||||||| |||||||||||| | ||||| ||| |||| |||| ||||||||
-tagatctttgtagacattcatttgttctcatgcaattcctgttggtttcatacttgttatgtggcaacacccattacattataattctgtgca-----atttcagAGGTGATCACTTGTGCGGAGTTCCATCCAACTCACTGTAATACACTAGCATATAGTAGCTCAAAGGGTACTATTCGGCTTATTGATCTGCGACAGTCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 9
-------gtggatca--ggtatcataaattga-accttctttaaaattatttttctttttttt-----tgtgtgtagctttggttgagcct-tgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
||| | | |||| | | | | |||| | | | | ||| | | || || | | || | |||| ||| | || |||||||||||| ||||||||||||||||| ||||| ||||| |||| || || |||||||| || || ||||||||||| || |||| |||| ||||||||
gtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatat---tcgttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCTATAGCAGTTCGAAAGGTTCAATTCGCCTGATTGATCTGCGCCAGTCAGC
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 7
gtggatcaggtatcataaattgaaccttctttaaaattatttttctttttttttgtg-tgtagctttggttgagccttgaccctatat----attattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
| | | | || | || || | | |||| | ||| || || || || |||||| ||| | ||||| ||| || |||||||||| ||||||||||| || ||||||||||| |||||||| | || |||||||| || ||||| || ||||| || ||| ||| ||||| ||||||||
----aatatttcctgtctatcattcatttgttctgggtgctattctactgtttaatgatgctgcattc-ttgagcattggacttatattccaattcttcttgcagAGGTGATAACATCAGCGGAGTTTCACCCTACCCATTGTAACATGTTAGCATATAGTAGTTCAAAAGGCTCAATCCGCCTTAATGATTTGCGACAGTCAGCMapped 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|22525826|gb|BU084637.1|BU084637EST: AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACTG AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
genomic: AAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACTGgtaagttttc ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttttgtgtgtagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
ccttgac putative branch site (score: 4)
tatatattattattgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggatcaggtatcataaattgaaccttctttaaaattatttttctttttttttgtgtgtagctttggttgagccttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - ccttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaccc