Sequence
atgc intronic sequence ATGC exonic sequencegtagttctttcttgcaagctgaaggcatttggcaatccatattatctctttttggttgaactgatctttgcattcctttataaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
Basic information
species | Glycine max |
transcript | GLYMA17G04580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 4
gtagttctttcttgcaagctgaaggcatttggcaatccatattatctctttttggttgaactgatctttgcattcctttataaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
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---gtactgtactgtagtattg-ggtactccataattcataatatctcaaggcacatgca-taatcccta-atgataccattactctcacagGTCATCAGGGGTCTAATTATGGATAAAGACAAAGGGAATTTGGTCAAAGCTGATCGTTTTGGTTACATTAAAAGGGCCATGCATGGCACCCAGATGCTTT
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 3
gtagttctttcttgcaagctgaaggcatttggcaatccatattatctctttttggttgaactgatctttgcattcctttataaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
||||| | | ||| || | ||| ||| ||| | | ||| || | | | | | | ||||| || ||||| ||||| || || |||||||| || || ||||||||||||||||||||||| ||||| || || || |||||||||||| ||||| | |
gtagtgcct----gcag--tgcacttctttcctaatacattgaagcactt-------aaatcacctctagtgatacaattgctgtgtcacagGTCATAAGAGGTCTTGTTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTT
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtagttctt---tcttgcaagctgaaggcatttggcaatccatattatctctttttggttgaactgatctt---tgcattccttta---taaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
| | | || | ||| |||| ||| || || | | || || | || | || ||||||| || | |||| |||| |||||||||||||| ||||||||||||||||| || |||||||| |||| ||||||| || ||||||| |||||||||||||| | |||| ||
gtgaaatctttatctgtgcaactagagaactttaaattgtgacaccattcttaaatttattgaatttgtattctctttca-tgtttttgagtgcattctgtttgattgttttgtgtagGTTATTAGAGGCCTTGTAATAGACAAAGAGAAAGGAAACTTGGTTAAGCCTGACAGATTTGGCTATGTAAAAAGGGCTATGCATGGTACAACAATGCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattatctctttttggttgaactgatctttgcattcctttataaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
aactgat putative branch site (score: 3)
attcctttataaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttctttcttgcaagctgaaggcatttggcaatccatattatctctttttggttgaactgatctttgcattcctttataaattgttcagGTAATTAGAGGCCTTGTCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT