Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgtagtgctgtagtacgaggttttcattttctcgagtttgtggttattcaagtgatgttgatatttggttccactaatttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
Basic information
species | Glycine max |
transcript | GLYMA17G35140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G35140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g35090.1 (Oryza sativa), 3'ss of exon 2
gtaggtgtagtgctgtagtacgaggttttcattttctc-gagtttgtggttattcaagtgatgttgatat----ttggttcca--ctaa--tttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
||| | || | | || || | | | |||| || | | || | | | | | | | | | ||| | || | | | | | ||| | || || || ||||| || || | || |||||||||||||| |||||||| ||||| |||||||| | | | | |||| ||| ||||
gtaaat-taattcggttaaactc--tcgccgctctctccgatgtcgcggccacgctgaagctttcgtcgtcggttcgattcgatgctgacctctctcggcgcagGTCTCGGACCGCGAGTTCCTCATCAGGGTCTCCTACATGGAGATTTACAACGAGGAAATCAATGACCTCTTGACGCTCGGGAGCGAGAAGCTGCCGATTC
upper sequence: GLYMA17G35140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G112745_T01 (Zea mays), 3'ss of exon 2
------------gtaggtgtagtgctgta-gtacgaggttttcattttctcgagtttgtggttattcaagtgatgttgatatttggttccactaatttgg-------tgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
| | | |||| | || || || | | | || | || || ||| || | || || |||||| || |||| || || ||||| || || || || ||||||||||||||||||||||| |||||||| ||||| | ||||| ||||| || | ||||
gtgtgttgattgctcgattatctgctccctgaacaagacattgttagattggttgctgcgattgttt--gtgctgcgcgtgagtgatttgttggatttgggtctgtttgggtcagGCTGACGAACGCGAGTTCCTCATCCGGGTGTCCTACATGGAGATCTACAACGAGGAAATTAACGACCTCTTGACACTTGAAGGCCAGAAGCTGAAGATTC
upper sequence: GLYMA17G35140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G033785_T01 (Zea mays), 3'ss of exon 2
gtaggtgtagtgctgtagtacgaggttttc-------attttctcgagtttgtggtta----ttcaagtgatgttgatatttggttccactaatttgg---tgcct----cagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
|| || | |||| | || | | | | || | || || | | | || || | || || |||||| ||||| ||| || || ||||| || || || || ||||||||||||||||||||||| ||||| || ||||| | ||||| ||||| || | ||||
gtgtgttgattgctcgattatctgctccccgaacaagacattgttagattggttgctgcgattgtttctgctgcgcgtgagtgatttgttggatttgggtctgcctgggtcagGCTGACGACCGCGAGTTCCTCATCCGGGTGTCCTACATGGAGATCTACAACGAGGAAATCAACGACCTCTTGACACTTGAAGGCCAGAAGCTGAAGATTC
upper sequence: GLYMA17G35140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G59540.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaggtgtagtgctgtagtacgaggttttcattttctcgagtttgtggttattcaagtgatgttgatatttggttccactaatttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
|| |||||| ||| | | | || | || | | | | | ||||| || | | | | | |||| |||||||| |||||||| || || ||||| |||||||| || |||||||||||||||||||| ||| | | |||||| || |||| | |||||||||
----gtatagtgc-atagaattattcagtgatctgt--gaagtaagaaaaagagtacagcttttgattcgtgtgtgttttgttctttgtttttagATATCTGATCGTGAGTTTCTCATCCGGGTTTCGTACATGGAAATTTACAACGAAGAAATTAATGATCTTTTAGCTGTTGAGAACCAGAGACTGCAAATTC
upper sequence: GLYMA17G35140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g08700.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaggtgtagtg--ctgtagtacgag-gttttcattttctcgagtttgtggttattcaagtgatgttgatatttggttccactaatttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
|| ||| | | || | | || | | || | || | |||| | | | | || || | | || | |||||| ||||||||||||||||||| ||||||||||||||||| || || || |||||||| ||||| ||||||| || || || |||||||| |||||||
gtattacttattgtttttgttgcaaacgttaccatggctattgttacttaaatcaattaggggtttcttatt---tatccattttaatgtttatattcttactttctcagACAGCTGATCGAGAGTTTCTGATTCGAGTTTCCTACATGGAAATTTATAATGAAGAAATCAATGATCTTCTTGCAGTAGAGAACCAGAAATTACAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtggttattcaagtgatgttgatatttggttccactaatttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
cactaat putative branch site (score: 2)
ttgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgtagtgctgtagtacgaggttttcattttctcgagtttgtggttattcaagtgatgttgatatttggttccactaatttggtgcctcagATGTCTGATCGAGAGTTTCTGATACGAGTTTCCTACATGGAGATCTACAACGAAGAAATTAATGACCTTCTTGTTGTTGAAAATCAGAAATTGCAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA