Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtgccacaggttattgacttacactattatgcacaatttaatgttcaatgctgagtttccttgtgttatatttgcagGAGATTATGGCTATGAAATTTAATGTCCTGGTGACTACTTATGAGTTCATCATGTATGACCGGGCAAGGCTTTCAAAAATTGATTGGAAGTATATCATAA
Basic information
species | Glycine max |
transcript | GLYMA09G39380.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39380.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 7
-----------gtaagtgtgccacaggttattgacttacactattatgcacaatttaatgttcaatgctg-----agtttccttgtg-ttatatttgcagGAGATTATGGCTATGAAATTTAATGTCCTGGTGACTACTTATGAGTTCATCATGTATGACCGGGCAAGGCTTTCAAAAATTGATTGGAAGTATATCATAA
| | || | || || ||| ||| | || | | | || || | ||| || || ||| ||||||||| || ||||| ||||||| ||||| || || || || ||||| || | ||||||||||| | | |||||||| ||||||||||||||| || || |
ttctctgacttcggaatcacccgcttactaatgcattatctgatttggaaccacctgctcacggattttgcttcaatattctttttgattaatcttgcagGAGGTTCTGGCTGTGAAATTCAATGTTCTTGTAACAACATATGAATTTGTTATGTATGACCGTTCCAAGCTTTCAAGAATTGATTGGAAGTACATTATTA
upper sequence: GLYMA09G39380.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 8
gtaag-tgtgccacaggttattgacttacactatta-tgcacaatttaatgtt-caatgctgag-----tttccttgtgttatattt-gcagGAGATTATGGCTATGAAATTTAATGTCCTGGTGACTACTTATGAGTTCATCATGTATGACCGGGCAAGGCTTTCAAAAATTGATTGGAAGTATATCATAA
||||| ||||| | ||| |||| | ||| || |||||| || | | |||||| |||| |||| | | ||| ||||| | || ||||||||||||||||| ||||| |||||||| |||||||||||||| || ||| ||||||||| ||||||||||||||||||| |
gtaagctgtgcaa------atttgcttattttgttagtgtccaattttctgctatagtgctgaaaatcctttctttgtcatgtgttttatagGAGGTGTGTGCCATGAAATTTAATGTCCTTGTGACAACTTATGAATTCATCATGTATGATCGTTCAAAACTTTCAAAAGTTGATTGGAAGTATATCATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actattatgcacaatttaatgttcaatgctgagtttccttgtgttatatttgcagGAGATTATGGCTATGAAATTTAATGTCCTGGTGACTACTTATGAGTTCATCATGTATGACCGGGCAAGGCTTTCAAAAATTGATTGGAAGTATATCATAA
atttaat putative branch site (score: 4)
aatttaatgttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtgccacaggttattgacttacactattatgcacaatttaatgttcaatgctgagtttccttgtgttatatttgcagGAGATTATGGCTATGAAATTTAATGTCCTGGTGACTACTTATGAGTTCATCATGTATGACCGGGCAAGGCTTTCAAAAATTGATTGGAAGTATATCATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG