Sequence
atgc intronic sequence ATGC exonic sequence...ttctaagaagctcttattgtattgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
Basic information
species | Glycine max |
transcript | GLYMA10G44150.2 |
intron # | 39 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
ttctaagaagctcttatt-gtattgctgttcaaaattgtgt-tttctatttgcc---tcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
| | ||| || ||| ||| ||| || | ||| | |||| ||| || | ||| || || ||| | ||||||||||||||||| || || ||||| ||| |||| ||||||||||||||||||
-----taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG-----------------------------------------------
upper sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 38
ttctaagaagctcttattgtattgc-tgttcaaaattgtgttt-tctatttgcctcatttttccctct-gccactctttttttatattcttg-ttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
| ||| | || | ||| || | | | |||| | | ||| | | | | ||| | | | | | |||| ||| || ||||| |||||||| || ||||| | ||| |||||||| ||||||||||||||||||
---tgaga-gtcctccctctatggcatactttacgttgtctgtgtctgtcatcgatagcatgttttctagtttataatgataaactttctcacttcttttgcagGGTTCAATTCCACTTTACGACTAGGGAATATTACTCATCATGAATATATTCAG-----------------------------------------------
upper sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
---------ttctaagaagctcttattgtattgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
| ||| || | | | ||||| | | | || | ||| | || || || | |||| | | || ||||| || |||||||| ||||| | |||||||||||| || |||||||||||||||
tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagaga----aagggagtaccaatgttctttaagc-----ttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG-----------------------------------------------
upper sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 3'ss of exon 37
ttctaagaagctcttattgt--attgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattct--tgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
|| || || | || | || | |||| | |||| | | || | ||| |||||| || | ||| || | | |||||||||||||| || ||||| | ||| ||| |||| ||||||||||| ||||||
----aatgagttcatgttattaatcgttgttaatcgttgttaatcgttgttatggaactttatcctctggtcagctacaaccaagctctattgcttttctgcagGATTCAATTCTACTTTACGACTAGGGAATGTTACCCATCATGAATACATTCAG-----------------------------------------------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|193490196|gb|FK453739.1|FK453739EST: TATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAAGATATCTATTCAG GATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTC
genomic: TATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAAGATATCTATTCAGgtatggctgt ... tcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
tttttccctctgccac CT-rich tract
tttttttatattcttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctaagaagctcttattgtattgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA
- - - - - - - - - - - tgctgtt