Sequence
atgc intronic sequence ATGC exonic sequence...attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
Basic information
species | Glycine max |
transcript | GLYMA05G35310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 2
attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
| | || | | || | | ||| | | | | | || | | ||| | |||| | | | | | || |||||||||||||||| || |||||||||||||| || |||| || || || || ||| |||
gtagacttaattagtgggtatttgtgtaatactgatgtgcattactttgtttcctaattttttttgtatattactgaatcacatatattgatattaacagGGACCACAATATGTCTGTACAAATTTCTGGACCTTCATTTGTACCAATTGCAGTGGAGCACA
upper sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
attgcattcttctga-acctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgt-tagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
|| | || | | | | || | | ||| || | || | | || | | |||| | | || ||| |||||||||||||||| ||||||||||||||||| |||||||| || || || || ||| |||
-acatatcttgctaatatgttacaagagtaatattttgttag-tgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
upper sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 3
-attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
|| | | | | | | | |||| | ||| | | | || | | || | | | | | | ||||||||||||||| ||||||||||||||||| || ||||| || || || || ||| |||
tatcttgctaatat-attatgagaataatgttttgttattgccttccctactgttccacctgaagaaaaaagcaagaacactgatatgctgatttgaacagGGACCACAATATGCCTGCACAAATTTCTGGACCTTCGTTTGTACCAATTGCAGTGGAGCACA
upper sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttg-ttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
| || || | | | |||| | |||| | | ||| | || | | | | || ||| | || || |||||||||||||||||| ||||| | ||||||||| |||||||| || ||||| || ||||||||
-gtaagtttttttttgctcttc------atttgatcatttccgataaaaattttgagagaacttaacgt-taacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
upper sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04210.t01 (Vitis vinifera), 3'ss of exon 1
---attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagac-tagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
||| | || || | | | | | ||| || | || | | || ||| | |||| | | || || | | || |||| || ||||||| ||||| |||||||||||||||||||| ||||||||||| | ||||| || |||||
aattttgtagtccaaagagctcaccaactacattcttca--ttaacttggaaagatgaaatatagtctatgatatgaaggc--taattttttccttccaaacagGGACCGCAATACGTGTGCACAAATTTCTGGACATTTGTTTGCACAACTTGTAGTGGGATACAMapped 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|193365877|gb|FK328982.1|FK328982EST: TGTAACAGCTTG GGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGT
genomic: TGTAACAGCTTGgtaggatttt ... ctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
ttaaatccttttttct CT-rich tract
attaaatcctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
- -gcattct
- - - - - -ctgaacc
- - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatta