Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgtttttctttggtgctacacttttccctgatcttattctgtgctttcagaccttatttttgattgacatgttaatttccgttgtcttgcttgatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
Basic information
species | Glycine max |
transcript | GLYMA08G16870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G16870.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44280.1 (Arabidopsis thaliana), 3'ss of exon 2
--------ttgtgtttttctttggtgctacacttttccctgatcttattct-gtgctttcagaccttatttttgattgacatgttaatttccgttgtcttgctt-----gatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
|| || | || || | | | | || ||| ||| | | | | | | |||| | | | |||| | ||| || |||| || || ||||| || ||||| || ||||||| ||| ||||| ||||| || || || |||||||| ||||||||||| |||||||| || || ||
gtaacttcttttggaacttttgagttttcaatcacacaaaatttgtagtcttgtgtaatttaaggtaaatctgagttgatgtaaaatgattttttgttctacttcatatgacagATTGATAGATTTGGGCATTTCAAAATTTGGCATGCTGCAGGATCCTTATTAGTTGCTATCTCATTTTCCTCTGTTTTTGGCGGTTGTTTGCCTTGTTCAC
upper sequence: GLYMA08G16870.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G60070.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttgtgtttttctttggtgctacacttttccctgatcttattctgtgctttcag--accttatttttgattgacat-gttaatttccgttgtcttgcttgatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
| | | |||| || | || | || | | | ||| || | | | || || || | |||| | | | | | || ||| || |||| || ||||||||||| |||||||| ||||||| ||| ||||| ||| |||| ||||| || ||||| || |||||||| |||||| | || ||
gtactctacttctctgtttctg-atttagtctttagcttgttgtttcttactagtggtgctaattcagtttgaggtagatgaatatggtcttctgttatggcagATTGATAGGTTTGGACATTTCAAGATTTGGCATGCTGCAGGATCATTACTGGTTGCAATCTCGTTTTCCTCCGTTTTTGGAGGTTGTCTGCCTTGTTCGA
upper sequence: GLYMA08G16870.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0156g00080.t01 (Vitis vinifera), 3'ss of exon 4
ttgtgtttttctttggtgctacacttttccctgatcttattctgtgctttcagaccttatttttgattga---catgttaatttccgttgtcttgcttgatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
| |||| || | || ||| | |||| || | || | | || || ||| | || | | |||| || ||||| ||||||||||||||||||| ||||| ||||||||||| || |||||| | ||||| || |||||||||| || |||||||| ||||| |||| ||||||
---ttttttcagttcttcaatcattttaatcctttctttttttttggtaaataaaactacagttagctgaaaataattttgccttcattgttttacttgacagATAGACAGGTTTGGACATTTCAAAATATGGCATGGGGCAGGATCTATTTTGGTTGCTGTTTCATTTTCCTCCGTTTTTGGCGGTTGCCTACCTTGCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttcagaccttatttttgattgacatgttaatttccgttgtcttgcttgatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
tgttaat putative branch site (score: 3)
tcttgctt putative PPT
ttatttttgattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgtttttctttggtgctacacttttccctgatcttattctgtgctttcagaccttatttttgattgacatgttaatttccgttgtcttgcttgatagATAGACAGGTTTGGACACTTCAAGATATGGCATGGTGCTGGATCTTTATTGGTGGCAATTTCATTTTCTTCTGTTTTTGGTGGTTGTTTACCATGCAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - -tggtgct
- - - - - - - - - - - - - ttccctg
- - - - - - - - - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg