Sequence
atgc intronic sequence ATGC exonic sequence...gcaaagtgaaggaagaataatttgctttctatttttttgcctgctcagttccattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
Basic information
species | Glycine max |
transcript | GLYMA15G02640.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
gcaaagtgaagga-agaataatttgctttct-atttttttgcctgctcagttccattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
| ||| | | || | || ||| || ||| | | || | ||| | || |||| || | || | | || |||| ||||||| || |||| || || || ||||| || ||||||||||| |||| |||||||||||||||||||| || || || |||| |||||||||||||
-attattgatgtttaagatgacctggaatctgatctttacacttactgtaattcatgtcctggtaatatgttgtgcat-gatgtaatttgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 7
---gcaaagtgaaggaagaataatttgctttctatttttttgcctgctcagttccattttaaaagtatcggttgagccttgaccctagatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
| | || | | | | | ||| | | | | || | || | | ||| || | | ||| | ||||||||| |||||||| || ||||| || ||||| || || ||||||||||||||||| || || ||||| || ||||| |||||||| |||| ||||||||
gctttcctttattgtttttatcacatattctttgagtttctactggtggcatctttgttgttagctactgat--agctatggttttg--ttctatcacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACCCACTGCAATACGTTGGCATATAGTAGCTCTAAGGGATCCATTCGACTTGTTGATCTGCGCCAATCAGC
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 9
------------gcaaagtgaaggaagaataatttgctttctatttttttgcctgctcagt-tccattttaaaa--gtatcggttgagcct-tgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
| || | || |||| || | ||| | | || | | | || || | |||| | || | |||| || | || |||||||||||| ||||||||||||||||| ||||| ||||| |||| ||| || ||||||||||| || ||||||||||| || |||| |||| || |||||
gtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccata---ttcgttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCTATAGCAGTTCGAAAGGTTCAATTCGCCTGATTGATCTGCGCCAGTCAGC
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------gcaaagtgaaggaagaataatttgctttctatttttttgcctgctcagttc-cattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
| | | || || | ||| | |||| || || | ||| | ||| | ||| || | | | || | |||||||||||| |||||||| || ||||| |||| |||||||||| | | |||||||| |||||||| || || |||||| | |||| |||| ||||||||
gtatgctacttctcctattttgttagatgttactttgtatggtcttaccattgattcatatgtcaacaacctccttac--ttttattatctatttttttcacgtttactgcttgtcgagcatgcttctaaatgctacatggtctgtgcagAGGTTATTACATCAGCTGAGTTTCATCCTATCCATTGTAATATGCTCGCATATAGTAGTTCAAAAGGCTCCATTCGTTTGATTGATATGCGTCAATCAGC
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 7
gcaaagtgaaggaagaataatttgctttctattt-ttttgcctgctcagttccattttaaaagtatcgg----ttgagccttgaccctagat----attattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
| | | | | |||| || || |||| | | ||||| | | |||||| ||| | || || ||| || |||||||||| ||||||||||| || ||||||||||| |||||||| | ||| |||||||| |||||||| || ||||| || ||| ||| |||||||| |||||
---------aatatttcctgtctatcattcatttgttctgggtgctattctactgtttaatgatgctgcattcttgagcattggacttatattccaattcttcttgcagAGGTGATAACATCAGCGGAGTTTCACCCTACCCATTGTAACATGTTAGCATATAGTAGTTCAAAAGGCTCAATCCGCCTTAATGATTTGCGACAGTCAGCMapped 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|11274020|gb|BF324388.1|BF324388EST: AGTTTTAATATTGTTGATGTAAAGCCCTGC-AATATGGAGGATCTGACAG AGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCAT
genomic: AGTTTTAATATTGTTGATGTAAAG-CCTGCAAATATGGAGGATCTGACAGgtaagcttga ... attattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttccattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
ccttgac putative branch site (score: 4)
tagatattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaagtgaaggaagaataatttgctttctatttttttgcctgctcagttccattttaaaagtatcggttgagccttgaccctagatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGC
- - -gtgaagg
- - - - - - aagaataa
- - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - ctgctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaccc