Sequence
atgc intronic sequence ATGC exonic sequence...gaaacaaaatataacgtttcatgattaagtttccatagactttttaattctcttattcttctattaactttggtgtgaacttattgtgctcttgttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
Basic information
species | Glycine max |
transcript | GLYMA11G06550.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06550.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g58410.1 (Oryza sativa), 3'ss of exon 4
--gaaacaaaatataacgtttcatgattaagtttccatagactttttaattc-tcttattcttctattaactttggtgtgaacttattgtgctcttgttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
|| || | | ||| | | || ||| | | || | || || || | ||| | ||||| || ||| ||||||||||||||||| || || |||||||| ||||||||||| | || || || | || | ||||| ||||| || || ||| |||| ||||||||
ccttgtcattatgttagattttgtttcttgattgccaggaaaaaaagactttatattctttagaagttgagtttcttaccaacttctt---tactttctgcagGGTTGTTAGCCAAGTAGAGTATCCCTCGTTGGTTGATTTGCGAGGTCTCCTCTTAGATCTTGTTGCCCAACTTTTGGGAGCTTTATCTCGTATCAG
upper sequence: GLYMA11G06550.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gaaacaa---aatataacgtttcatgattaagtttccatagactttttaattctcttattc----ttctattaactttggtgt--gaacttattgtgctctt--gttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
| ||| ||| | | | | | || | | | | ||| || | || || || ||| | | | | | ||||| | ||| ||||||||||||||| || ||||| || || ||||| ||||||||||| || ||||| ||||| |||||||||||| | ||||| || |||||||| ||
gtagtgatttcagaatctggaacggttgaattttatatgattcgctaaacacttcttttatcctttggcattcctttttcgagttgtaaaaacctgaatttctaagttctgggtgcttctccgttacagGGTTGTTAGCCAAGTGGAATACCCATCGCTGGTCGATTTGAGGGGTCTCCTTCTTGACTTGGTTGCTCAACTCCTGGGTGCACTGTCCCGTATTAG
upper sequence: GLYMA11G06550.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0083g00750.t01 (Vitis vinifera), 3'ss of exon 5
gaaacaaaatataacgtttcatgattaagtttccatagactttttaattctcttattcttcta-ttaactttggtgtgaacttattgtgctcttgttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
|||| | | | | | | | | | | | |||||| | | || || || | ||| | ||||| | | || ||||| ||||||||||||||||||||||||||| ||||||||||| |||| ||| | || ||| |||||||||||||| | |||||| |||| || |||||
-gtgggaaatgttgtaatctttattctgttgtactttaagctcattattctcatttgctcatagttttccttgttatgaacacaacatttattttctgcagAGTTGTTAGCCAGGTTGAATATCCCTCATTGGTTGATTTGCGGGGACTTTTGCTAGACCTAGTTGCTCAACTCCTTGGTGCTTTATCTCGGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctcttattcttctattaactttggtgtgaacttattgtgctcttgttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
tattaac putative branch site (score: 1)
ctcttgtt putative PPT
ttattcttctattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaacaaaatataacgtttcatgattaagtttccatagactttttaattctcttattcttctattaactttggtgtgaacttattgtgctcttgttgcagGGTTGTTAGCCAGGTTGAATATCCCTCACTGGTTGATTTGAGGGGGCTTCTTCTGGACTTAGTTGCTCAACTCTTAGGTGCTCTATCCCGTATCAG
-aaacaaa
- - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgtgc