Sequence
atgc intronic sequence ATGC exonic sequencegtaaattgaggagttcctgatttaattctttattgctttgacacttcgtgatttgctatggctttagtgtttgttcttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA05G01800.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G01800.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G50110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaa-attgaggagttcctgatttaattcttta----------ttgctttgacacttcgtgatttgctatggctttagtgtttgttcttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG
||| ||| | |||| | | | | | |||||| | || ||| || ||| | | ||||| | || |||| |||||||||||||||||||| ||||||| | ||||| |||||| | ||||| ||||||||||| || ||
gtattatttacaagtttcaagtagggtagtgcaagaaacaaagttgctt-attagttagtg-ttcaaagtggatctga--gttgtttgttatgaattttcagCTGAATATTGTCTTCCTCTGGTTCGGATTGGTGGATTGTTTGTAGCTGCTAAGGGTCATGACCCAAAG
upper sequence: GLYMA05G01800.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g07700.t01 (Vitis vinifera), 3'ss of exon 4
gtaaattgaggagttcctgatttaattctttat-----tgctttgacacttcgtgatttgctatggctt----tagtgtttgtt-cttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG
|||| | | | ||| ||| || | | || ||| | | | |||| |||| ||||| || || | ||| ||||||| || ||||||||| | |||||||| ||||| |||||| | ||||| || ||||||||||| |
gtaattattagtatgcctttccagatttcttttgaatatatttaagtgtttcagaagtcatcactgcttgagatagtttttgtggtttatttctttttcagCTGAGTACTGTCTTCCTCTAGTTCGTGTGGGTGGTTTGTTTCTAGCTGCGAAAGGTCATGATCCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgacacttcgtgatttgctatggctttagtgtttgttcttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG
ctttgac putative branch site (score: 4)
catttcc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattgaggagttcctgatttaattctttattgctttgacacttcgtgatttgctatggctttagtgtttgttcttgttgcatttccagCTGAATATTGTCTTCCTTTGGTTCGTGTCGGTGGGTTGTTTATTGCTGCCAAGGGTCATGATCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC