Sequence
atgc intronic sequence ATGC exonic sequence...agaatttatttgataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
Basic information
species | Glycine max |
transcript | GLYMA10G15900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
----agaatttatttgataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaact--ctttacaattcatact--ttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
| |||||| ||||| ||| | | | | ||| || | | || | | | ||||| | || || | | | | |||||||||| || | ||||| ||||| |||||||| || ||||| ||||||||||| || || ||||| || ||||| ||||||||||| || || | |
gacatgcatttatgtgatattaactt-------tcgttgacccaacc-tattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
--agaatttatttgataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
| || | | | | ||| | | | || | ||| | | ||| | | | | | | || | | || |||| || || || |||| ||||| ||||||||||| || || || ||||| |||||||| ||||| || || ||||| |||||||| ||||| ||||| ||
ttaacggccgagtgttcatgcttggttttacttcttaactgttttgaat-tatatccttccaatttatttctgcaatttatatttgttttgttttctg-cagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA
upper sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
--agaatttatttgataccaaccaatagaagctgat--aatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactt-tgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
| ||| | | | || | || | | || | | | | || ||| | | | | |||| || | || || |||||| ||||| || || || | || ||||||||||| ||||| ||||| | ||||| ||||||||||| |||||||||||| |||| || ||||| |
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagttttcttgaatt---ggttcttact-ttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC
upper sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------agaatttat---ttgataccaaccaat-agaagctgata-atttagtagtatatctatttcta----------tattttctcattctcaac--tctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
| | ||| ||| | | ||| | ||| ||| |||| | | | || | | | ||||| ||| | | | |||| | || | | | ||||||| || ||||||| ||||| ||||| ||||| || ||||| ||||||||||| || ||||||||||||||||| |||||||||||||| ||||| ||
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
upper sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
agaatttatttg-ataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
| || | || || | || | | || | ||| || | | | || | | ||||| | | |||| ||||||||| ||||| | || |||||||| |||||||||||||| || ||| | || ||||||||||| |||||||| || || || || ||||
-tcacttgtgtgtgtatgtatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgactggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
tatttctatattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatttatttgataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaactctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - -ccaacca
- - - - - - - - - - - - -gaagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caattca