Sequence
atgc intronic sequence ATGC exonic sequence...acaatgaccctctcccctagcatagcaagggccgaggagccttttggcactgggctatgttagttttttgttgatttcttttgtactgttttccttacagGACTGTTGAAGTCCCTGGCTCTCGTATTGTAATCATAGAAGGCATCTATGCCTTAAGTGAAAAATTACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
Basic information
species | Glycine max |
transcript | GLYMA05G07610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 3
acaatgaccctctcccctagcatagcaagggccga---ggagccttttggcactg-ggctatgttagttttttgttgatttcttttgtactgttttc-cttacagGACTGTTGAAGTCCCTGGCTCTCGTATTGTAATCATAGAAGGCATCTATGCCTTAAGTGAAAAATTACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
| | ||| ||| || || | | |||| | | || ||| | || | ||| | | || | | | || | | |||| || ||||| |||||| ||||| | ||||| ||||| |||||||||||||| || |||||||| |||||| || | | || || |||||||||||||||
------gtagtttgtccttaaataataattcccagtttgtcactttttagtattgtaaatatat-ggtcatatgtctttatgttatcttttcttatggcaaacagAACAGTTGATGTCCCTAGCTCTAGGATTGTTATCATTGAAGGCATCTATGCATTGAGTGAAAAGTTACGATCTGTATTGGACCTACGTGTTTCTGTCACT
upper sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------aca-atgaccctctcccctag--catagcaagggccgaggagccttttggcactgggctatgttagttttttgttgatttcttttgtactgttttccttacagGACTGTTGAAGTCCCTGGCTCTCGTATTGTAATCATAGAAGGCATCTATGCCTTAAGTGAAAAATTACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
||| | | | | | | | | | | || | || | | || | | | || | |||||| || | || || || |||| || ||| ||||||| ||||| || |||||||||| ||||| || ||||| || |||| |||||||| ||||||||||| |||||||||
gtatatatattcttcgttggtgcatttactactatttcaaacttgtggacagacggcgttatacttgaattcctgggaaccacttgttagttgataagagctacacagctgcaatgacttatcagtttcttc------gtgctttgtatagAACGCTTGAGGTGCCTAGCTCTCGCATTGTTATTCTAGAAGGCATATATGCTTTGAGTGAGAAGCTACGGCCTTTGCTAGATCTTCGTGTCTCTGTCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcactgggctatgttagttttttgttgatttcttttgtactgttttccttacagGACTGTTGAAGTCCCTGGCTCTCGTATTGTAATCATAGAAGGCATCTATGCCTTAAGTGAAAAATTACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
tgttgat putative branch site (score: 4)
tttcttttgtactgtt CT-rich tract
tatgttagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaatgaccctctcccctagcatagcaagggccgaggagccttttggcactgggctatgttagttttttgttgatttcttttgtactgttttccttacagGACTGTTGAAGTCCCTGGCTCTCGTATTGTAATCATAGAAGGCATCTATGCCTTAAGTGAAAAATTACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
-caatgac
- - - - -ctctccc
- - - - - - - - - - - - - - - - - - - -ccttttg