Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaatattggtttataaagcttctatataagtttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
Basic information
species | Glycine max |
transcript | GLYMA12G04210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------gtaagtaatattggtttataaagcttctatataagtttgttgcaga---aaatgttattattgaattcttctataccattatcttattt---aacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
| | || |||| || | ||| || |||| ||| ||| | | | | | | | | || |||| | |||| || || ||||| || |||||||||||||||||| |||| ||||||||||| | ||||| | | | | |||||||| | | || ||| || |
gtgatttttttgaccctttgagttttaacttattgtatttttttat--gtctgttatagacttgaattggctcacaggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG
upper sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaatattggtttataaagcttctatataagtttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
|| || | | | | || ||| || || || ||| | | || || || ||| | | | ||||||| || |||||||||||||| ||||| |||||||||| ||||| || |||||||| || | ||| | |||| ||||||| |||| ||||| |||| |
gtgagctgctgagactgttt---ttcctttattggt--atttcatttcatgctgctttttcat--ttacgtacttgcaatctttataacagGTACCAAGTTGTCAGAAGACAGCAGAAAATATGGTGTTGAAAACACTTGTACCAGTGGCAGTACCTTATCTAAAGCTGCATTAAGCTTTGCTAGAGCTCG
upper sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaagtaatattggtttataaagcttctatataagtttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
| || ||| ||| || | || || | |||| | | | | | ||| || || | ||| | | ||| ||| |||||||||| |||||||||||| ||||||||||||||| |||||||| |||||||| |||||||| | || | ||||||| | | || || ||||| |
gtgtgttggtgaaacttttgattttgttttttactattataattcaaatg-aatgcaaaggacttgact-ttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCGMapped 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|4290155|gb|AI441578.1|AI441578EST: TCGTGGTGTAGAAGGTTATATTGTTACTGGATCCAAGCAAGTGGAAATAG GAACAAAGTTGTCAGAAGATAGCAGGAAAATATGGTGCAGAAAATACATGT
genomic: TCGTGGTGTAGAAGGTTATATTGTTACTGGATCCAAGCAAGTGGAAATAGgtaagtaata ... tatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAA-TATGGTGCAGAAAATACATGT
EST:
gi|14008667|gb|BG725271.1|BG725271EST: GGATCCAAGCAAGTGGAAATAG GAACAAAGTTGTCAGAAGATAGCAGNGAAATATTNGGTGCAGAAAATACAT
genomic: GGATCCAAGCAAGTGGAAATAGgtaagtaata ... tatttaacagGAACAAAGTTGTCAGAAGATAGCAG-GAAATA-T-GGTGCAGAAAATACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
tcttattt CT-rich tract
aaaatgttattattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaatattggtttataaagcttctatataagtttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC