Sequence
atgc intronic sequence ATGC exonic sequenceTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagtgtttggctgcaataccttgttttcttgttagctttagcataggtttcttggtatgaggttaaaaggtcatgaatgtccttactcattggc...
Basic information
species | Glycine max |
transcript | GLYMA20G36180.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36180.1 (Glycine max), 5'ss of exon 5
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 5
TAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagtgtttggctgcaatacct-tgttttcttgttagctttagcataggtttcttggtatgaggttaaa-aggtcatgaatgtccttactcattggc
||||||||||| |||||||| |||| ||||| || ||||||||||||||||| ||||| ||||| | | ||||||||| || | | | ||| |||||| || || | || | | || | | | | || || ||| | | || | | || || | | | ||
CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCTTTTGATGTTCTGTCAGAATTTGATGCTAATAATGAAGCCTCTGGTAGCCCCATGTTGgtaaggacttgacccgcacctttatttatattatttagacatgttgcatgtacaattccatctccaatgtcatttacgtaatactcaaagtcaaactgtg--
upper sequence: GLYMA20G36180.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 5
TAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgta---atttagtgtttggctgcaataccttgttttct--tgttagctttagcataggtttcttggtatgaggttaaaaggtcatgaatgtccttactcattggc
||||||||||| |||||||| |||| ||||| || ||||| || |||||||| ||||| ||||| | | |||||||| || | | | ||||||||| | || | | || || || || | |||| || || || | | | | | || | | || ||| | || ||
CAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATGAAGCCTCTGGTAGCCCCATGCTGgtaaggacttgatctgcaccttatttatattagttacacatgttgcctgtacaattccctctccgatgtcat-ttgggtaatactcaaagtc---aaacagtgc-
upper sequence: GLYMA20G36180.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 5'ss of exon 5
TAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgta------atttagtgtttggctgcaataccttgttttcttgttagctttagcataggtttcttggtatgaggttaaaaggtcatgaatgtccttactcattggc
||||||||||| |||| |||||||||||||||||||||||| |||||||||||||||||||||| ||||| |||||| || | ||||| ||||||||| ||| | | || | | || | |||| | ||||| | || | ||||| | | | | ||| || | | |
AAGTGTTGTTGTTACACCTACTTTGGACTGGAAACTCCATGCTCTTGATGTTCTATCAGAGTTTGATGGGAGCAATGAATCTGCAAGTGGACCTATGCTGgtacacatcattcactattggtgttcactttcttgat--cttgtcaatttgaaagccattttctcccccaaaatcttagaattcaaacctgctgtcatattt----
upper sequence: GLYMA20G36180.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 5'ss of exon 5
TAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagtgtttggctgcaataccttgttttcttgttagctttagcataggtttcttggtatgaggttaaaaggtcatgaatgtccttactcattggc------
|||||||||||||| |||||| |||||||||| || ||||||||||| |||||||| |||||||| || || |||||| | |||| | || ||||||| | || | ||||| | | || || || | || ||| ||||| | ||| | | || | ||| | |
CAGTGTTGTTGTCACTCAAACTCTGGACTGGAAGCTGCATGCTTTTGACGTTCTATCTGAGTTTGATGGCCATAGCGAAGCTGCTACTGGGCCCTTGTTGgtaatcaa----tttatttcaatatgatccctgaatgc-agtttctttttgtcttgcttt-tatgaattccaaacttatttaacatttttaattaaaaattttctgMapped 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|37997477|gb|CF809066.1|CF809066EST: TTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGGCAAATGCTG CAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAA
genomic: TTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagt ... ttctattcagCAATATGCTTGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATGAAGCTTCCTCTGGACAAATGCTGgtaatttagtgtttggctgcaataccttgttttcttgttagctttagcataggtttcttggtatgaggttaaaaggtcatgaatgtccttactcattggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG