Sequence
atgc intronic sequence ATGC exonic sequence...gtcgtcatgaattttggccagtttgaattgaaaactctttttttcttaatatttgttatttatttatttttttgtttattttgggttttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG
Basic information
species | Glycine max |
transcript | GLYMA08G38190.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------gtcgtcatgaattttggc-cagtttgaa--ttgaaaactctttttttcttaatatttgttatttatttatttttttgttt--attttgggt-------------tttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG------------------------
|| || |||| | | | || | || ||| | | ||| |||| ||| || || ||||||| | | | || |||| | | || || |||||||||||||||||||||| |||||||||||||| ||||||||| |||| |
gtaagtatataattaagaatccaataagttgtgattaggaattaattaagtactgttttgtgatttgccattgactaaaggtcaaagacttcaatactattactattgaagttttggtttttgttttgttctaagtgtaagtattaatgtaaatatttgattgatgtagACATAGATGGACGGGAAGATATGAAGCACATCTATGGGATAATAGCTGTAGGAGAGAAGGTCAGGCCAGGAAGGGACGTCAAG
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 2
-gtcgtcatgaattttggccagtttgaattgaaaactctttttttcttaatatttgttatttatttatttttttgtttattt-tgggttttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG------------------------
| || ||||||| | | ||||| ||| || || | | |||| ||| || |||| | | || ||| | |||| || ||||||| |||||||| |||||||||||||||||||||||||||||| | || |
caaacttttgttttttggctg--tgggtgggaaaaagatttgacatttgatttaagcaattttgatatgagttcaattatatgtatgtgttgattgatgcagACATAGATGGACTGGAAGATACGAAGCGCATCTATGGGATAACAGCTGTAGGAGGGAAGGTCAAGCCAGAAAAGGACGTCAAG
upper sequence: GLYMA08G38190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 2
-gtcgtcatgaattttggccagt--ttgaattgaaaactctttttttcttaatatttgttatttatttatttttttgtttattttgggttttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG------------------------
| ||| | | | | ||| ||| || || || | | | | | | | | | ||| || ||| || ||| | |||| ||| | |||||||| ||||||||||||||||| |||||||||||| | || | ||||
taacagcattcactgtttcaagtgtttgggttcctgggaacttgttcatcagtgtgtatagggaacaaactagtttatt-gctttctgtattgct--ttgcagACACAGGTGGACGGGTAGATATGAAGCGCATCTGTGGGATAACAGCAGCAGAAGGGAGGGCCAGGCCAGGAAGGGGCGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatttgttatttatttatttttttgtttattttgggttttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG
tcttaat putative branch site (score: 3)
ttttgttc putative PPT
atttgttatttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgtcatgaattttggccagtttgaattgaaaactctttttttcttaatatttgttatttatttatttttttgtttattttgggttttgttcaccgcagGCACCGATGGACGGGAAGATATGAAGCGCATCTATGGGATAACAGCTGTAGGCGAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg