Sequence
atgc intronic sequence ATGC exonic sequence...aggttacattacatattctgaattcgtgatccctaacatttattcaattatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA15G03360.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 9
--------aggttacatta-catattctgaattcgtgat----ccctaacatttattcaattatcttct--ttgctccttccttctctctcccttgtgtc----tgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
| || || || |||| | || | ||| || | || | | | | || | ||| | || || | | || |||||| | ||||| || ||||| | | || || |||| |||||||||||| | |||||||| ||||| || || |||||||||||||||||
gttagtcaaatttctatgggtatgttcttttatgatggtagtgtactagtatagtcctgaactcctgatggtcgattttttttcttctaagcattatgcaatcatattttatatttcagAAATTCAAGCAACACCCTGCTGTCAGGACAATTTTGGATGGTGGAACAGTTCTTCAGTATGGTGCTCGTACGTTGAATGAAGGTGGTTTTCAA
upper sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G032222_T03 (Zea mays), 3'ss of exon 9
-aggttacat-tacatattctgaattcgtgatccctaacat-ttattcaattatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
|| ||| | ||| | | ||| | | | | | | ||| | | | |||||| ||||| | || | | |||||| | ||||| || ||||| ||| | | || ||||||||||||||| ||| |||||||| || || ||| | |||||||||||||| |||
aagattaaggatgggtatattagaagactgactgatttcctatgaattaataaatagaatgaacctagttttctctaaatattgtg-caatcatattt--cagAAATTTAAGCAGCACCCTGCTGTTAGAAAACTTTTGGAAGGTGGAACAGCTATTCAGTATGGTGCACGTACTCTCAATGAAGGTGGTTTCCAG
upper sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 9
aggttacattacatattctgaattcgtgatccctaacatttattcaattatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
||| | |||| | || | | | |||| | | | | | | || | | | | || | | ||||||| || || |||||||| |||||| | |||||||||| || || | |||||||||||||| ||||||||||||||||||||||||
------------gtatg-tcaatttctcataacgatagacttttcagcggttactacaaatacatttctaaaac-ccatcatttttatcctc-caaatagAAACTCAAACACCATCCTGCTATTAAAGGCATCTTGGAAGGTGGTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAG
upper sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0102g01110.t01 (Vitis vinifera), 3'ss of exon 9
---aggttacattacatattctgaattcgtgatccctaacatttattca-attatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
| | | ||| | | || | | | ||||||| || || | || | | ||| ||| ||| || | | | | || | | | ||||||| || ||||||||||| || ||| | |||| ||||||| || ||| |||||||||| ||||||||||| ||||| || |||||||||
ctggaagtgtagtgtctatcttaattt---gcttgtaagcatttatccatgttttgctcgtgatttcttgcttatctttctatgttatgtttccttctaat-agAAACTTAAACATCATCCTGCCATCAAACCTCTTCTCAAAGGTGGGACTGTTCTCCAGTATGGTGCTCGCACTTTGAATGAGGGCGGTTTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
ttctttgctccttcct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggttacattacatattctgaattcgtgatccctaacatttattcaattatcttctttgctccttccttctctctcccttgtgtctgtcttggtcaccagAAACTAAAGCATCATCCTGCAATTAAATCATTTCTGGAAGGTGGAACAGTTATCCAGTATGGAGCTCGCACTTTAAATGAAGGTGGTTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - tgaattc
- - - - - - - - - - - - - - - -cctaaca