Sequence
atgc intronic sequence ATGC exonic sequence...tatctcacagttgaatgcatttttgtgttttctaaatcaaaaggcattggatttgtgcaccattcattgatctgatagctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
Basic information
| species | Glycine max |
| transcript | GLYMA09G03560.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g46240.1 (Oryza sativa), 3'ss of exon 3
tatctcacagttga-atgcatttttgtgttttctaaatcaaaaggcattggat--ttgtgcaccattcattgatctgatagctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
| | || | || |||| || || || | || | | | || || |||| | | || | | |||||||| || | ||||| |||| || || || ||||| || ||||||||||||||||||||||| ||| | | |||||||| || |||||||| ||||| |
---attatagacaacatttatttacttggcactatgcgcataatatgtaaaatggtggagatgcacatatgctaatgattcttacttcattttgtgatttcagATCCATGCAGCTGGCTTCTTAAACCCCACTCCAATTCAAGCTCAAACATGGCCTGTTGCACTGCAAAATCGGGACATAGTAGCTATTGCCAAGACAGGAT
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G703415_T02 (Zea mays), 3'ss of exon 4
tatctcacagttgaatgcatttttgtgttttctaaatcaaaaggcattggatttgtgcaccattcattgatctgata--gctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
||||| ||| | ||| | || ||| ||| || | | |||| || || || ||| | | || ||| |||| || | |||||||| |||| ||| || ||||| || |||||||||||||||||||| || ||| | |||||||| || ||||| || ||||| |
--tctcattgtttgcaaccaatttttacttgctatggaaaataccaattatctgctgcaggtgggcatgcccttatgatgcttattcgttttttcatttaagATCCATGCAGCTGGTTTTTCAAATCCCACTCCAATTCAAGCTCAAACATGGCCTGTTGCGCTGCAAAACCGGGACATAGTAGCTATTGCTAAGACAGGGT
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g00470.t01 (Vitis vinifera), 3'ss of exon 3
-tatctcacagttgaatgcatttttgtgt-----tttctaaatcaaaaggcattggatttgtgcaccattcattgatctgatagctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
| |||| | | || | || | |||||| | | | |||| | ||||| |||| ||| | | || | | ||||||||||||||| ||||||||||| ||| |||||||| ||||| || |||||||| |||||||||| ||||| ||||| || ||||||||||||||||| |
ttttctcgaatctactctcaatgatggatgggaatttctacct---gatctgcttgattctcttgcatgtcatt-atct-atatgtaatttttatt-ttgtttcagATATATTCGGCTGGTTTCTCTTCTCCTACACCAATTCAGGCACAGACATGGCCAATTGCACTACAGGGTAGGGACATTGTGGCAATTGCCAAAACAGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggatttgtgcaccattcattgatctgatagctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
atctgat putative branch site (score: 4)
ctctcgtttc putative PPT
attcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctcacagttgaatgcatttttgtgttttctaaatcaaaaggcattggatttgtgcaccattcattgatctgatagctgccatatactctcgtttcagATATATTCTGCTGGTTTCTCAAGTCCAACACCAATACAGGCTCAAACATGGCCTGTTGCACTACAAGGTAGAGACATAGTCGCAATTGCCAAAACAGGCT
- - - - - - gaatgca
- - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatac
