Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatttgtggtttttgctttcacttagatgtttaatttggcatgttgctgatgaattatatctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
Basic information
species | Glycine max |
transcript | GLYMA15G08090.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 4
gtttgtatttgtggtttttgctttcacttag-atgttta-atttggcatgt-tgctgatgaattatatctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
| || || | | | | | | ||| || ||| || ||| |||| | || | ||| | |||| |||| ||| ||| | | |||| ||| || || | |||||||| | | ||| || ||||||||||||||||||||||||| ||| |
-gtaacatcactgttcagtaatagtattaattatgattgcattctgcttgtctgctcacactttgataccgttttccagGGAATTATGATATGATTCAACATCCAAGGAATGCCAGCGAATTTTCAAAGGCAAATGCATGTTTTTATATGTTTGTAGATGAAGAAACAGAGGCTTATGT
upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 4
--------------------------------gtttgtattt---gtggtttttgctt-tcacttagatgtttaatttggcatgttgctgatgaattatat-ctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
|||| | ||| || || ||||| ||| | ||| |||| | | || ||| | | |||||||||| ||| ||| | | || | || || ||||||| |||||||| | | |||||| ||||||||||||||||||||||||| ||| |
gtatgcatcacttttcgctaatagtatccactatttgccctaaaaaaggtcttcactgatcactgtgat-tgcaatgaatttctctgctcacta-ttgtataccaccgctcagGAAATTATGATATGATTCAGCATCCGAGGAACATCAGTGATTTTTCAAAGGCAAATGCATGCTTTTATATGTTTGTAGATGAAGAAACAGAGGCTTATGT
upper sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 4
-----------------------gtttgtatttgtggtttt------tgctttcacttagatgtttaatttggcatgttgctgatgaattatat-ctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
|| | | | | | | || |||||| ||| | ||| |||| | | | ||| | |||| |||||||||| ||| ||| | | || | || || ||||| | |||||||| | | ||| ||| ||||||||||||||||||||||||| ||| |
gtatgcatcacttttcactaatagtatccactctttgccctaaaaaatgtcttcactgtgat-tgcaatgaatttctctgctcactattcgtataccgttgctcagGAAATTATGATATGATTCAGCATCCGAGGAACATCAGTGAATTTTCAAAGGCAAATGCATGTTTCTATATGTTTGTAGATGAAGAAACAGAGGCTTATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcacttagatgtttaatttggcatgttgctgatgaattatatctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
tgctgat putative branch site (score: 3)
ttagatgtttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatttgtggtttttgctttcacttagatgtttaatttggcatgttgctgatgaattatatctgttgttcagGAAATTTTGACGAGATAAATGAGCCAACAAATATAAGTGATTATTCAAAGGAGACAGTATGCTTCCTTATGTTTGTAGATGAAGAAACAGAGAAATATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA