Sequence
atgc intronic sequence ATGC exonic sequenceTTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag
Basic information
species | Glycine max |
transcript | GLYMA12G04820.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 9
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag
|||| ||||||||||| || || || ||||| ||||| || |||||||||||||| ||| |||| |||||| | || || || | || ||| | || ||| ||| || | ||| | | | | | | ||| | ||| | ||||| | | | | || || | | | | ||| |||| | ||
TTACCAATTTCATGTCAGACATAGCAGATGAATTCAAGATAGTTGTTGTTGAAGCTATACGATCTCTATGCCTTAAGTTTCCCCTGAAGTATCGTTCAATgtatgtaaatcttaattcggtgttgatgacatttacattcttttagtgccgtatgt--tttgactatcagttgcatttgg-tgtccaatgctcttcatttttttttcttctatag------
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttc--ccccagaagttacatatttcatttgaatgtttt---tcctagatgaatggtctaaattactggtttcttttctgttattattttcag
| || || || ||||| || || ||||||||||| || |||||||||||||||||||||||||| || |||||||| |||||| | |||||| | || ||| |||||| | || || | | | || | | || ||| | |||||| | | | || | | | || || |
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag--------------------------------
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 9
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag
| || || || ||||| || || ||||||||||| || |||||||||||||||||||||||||| || |||||||| |||||| | |||||| | || ||| |||||| | | | | | | | | |||| |||| | | | ||| | | | | ||| || | | ||| || |
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCTCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcatgtcttcttgcgctagtctt--------gttaaatatcata---aactacctttttcatctataagcattaatttccatttatctgttttag------------
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 8
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgttt---ttcctagatgaatggtctaaattactggtttcttttctgt-tatta--ttttcag------
| || ||||| ||||| |||||||||||||||||||||||||| || || || ||||||||||| | || |||||||||| | ||||| ||||| ||| |||| | | | | | ||| || ||| | || | ||||| |||||||| || | | | || | | | ||| || | | | ||| | ||||||
TAACTAATTTTATGTCAGATATTGCTGATGAGTTCAAAATTGTGGTCGTGGACGCAATAAGATCGTTGTGTGTGAAATTCCCACTGAAATACAGATCCTTgtaagtaaagttttagggtttgttatttgtagttttggtctcgagcatttctatttt-tttgaatgattaaatatgttatggtatctttttagcatttggcttatgattgatctatcaccttttcatttgtag
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 9
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag------------------
|||||||||||||||| |||||||||||||| |||||||||||||| || ||||| || |||||| | |||||||| || ||||| || |||||| | ||| ||| || || | | | | | || | | | || | ||| |||| |||| ||| || ||||| || |||| | | || | | || || |
TTACAAATTTCATGTCAGATATTGCTGATGAATTCAAAATTGTTGTAGTGGAAGCCATCAGATCATTGTGCTTGAAGTTTCCTTTGAAGTATAGAGCCTTgtaagtg-------atatcctgtttttgatgtcat--cattaaaacatttgggttttatttttatgtcttttttaaatgaacagtgtaaaatgtttccgtcatgtgaaatagaataaccctttttcccttgcttttcag
upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 5'ss of exon 9
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtat-atgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag
| || || |||||||| |||||||||||||||||||||||||| || || ||||| || | || || || | || |||||| ||| ||| | | ||||||| | ||| | | ||||| | || ||| || | | | | ||||| | || | ||||| ||| || || ||| |||
TCACGAACTTCATGTCCGATATTGCTGATGAGTTCAAAATTGTGGTGGTGGAAGCCATCCGCTCTCTTTGTCTCAAGTTCCCTCAAAAGTATCGCGCATTgtgagtttcgcaaaaatataaacctataaacctattgt-----gaatatataaacctattgtgaatatatt-----gtagaatgttct---ttgtgatatttccttcggttcc---------Mapped 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|208300498|gb|GE100263.1|GE100263EST: CAATAAGATCTACTATGCTTGAAATTCCCTTTAAAATATAGATCTCT GATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAA
genomic: CAATAAGATC-ACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatat ... ttattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA