Sequence
atgc intronic sequence ATGC exonic sequence...tgatgttgctgaaatttcttctgtgttctatcttttgtttgcatattgctatcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
Basic information
species | Glycine max |
transcript | GLYMA15G06110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G06110.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g37600.1 (Oryza sativa), 3'ss of exon 1
-tgatgttgctgaaattt-cttctgtgttctat-cttttgtttgcatattgctatcatgtaat-aatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
| | || | | ||| | || || ||| |||| | | ||| | || |||| | ||||| | | |||| | | |||| | |||||||||| |||||||| ||||| ||||||||||| |||||||| ||||||| || ||||| |||||| |||| || | || |||||||||
actgtatgcatgctctgtgctttgatattttacgttttcacacccataaggattgcatttgatcaatggcattg-ttgtgt-tggtttctgctgcttc--acagGCATCTGGTAACTCAAGTGCTCTCTTCCTGACTGCTGCAGCACAAAATCTCTTGTGTCTGAAGTTAGCTGAGGAGATTGGTGTTAAGATTGCAAACCCAT
upper sequence: GLYMA15G06110.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g29430.1 (Oryza sativa), 3'ss of exon 1
tgatgttgctg-aaatttcttctgtgttctatcttttgtttgcatattgctatca----tgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
|||| ||| || | | | ||| |||| | | || ||| ||| | | ||| || || | | || | | | |||| | ||||||||||| ||||| || ||||||||||||||||| |||||| || |||| | || |||||||||||||||| | || ||| |||| ||||
---tgtttctgtgcatcctatacttctgttattcattgtatacgcatcatcttcagaaatgtttttacagagtatctagttttcttctcctat--tttttaacagGCAGCTGGTAACTCAAGTGCGCTCTTCCTAACTGCTGCAGCACAAAATTTGTTGTGCTTGAAGCTAGCAGAGGAGCTTGGTATTATCGTTGCAAATCCAT
upper sequence: GLYMA15G06110.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G040933_T02 (Zea mays), 3'ss of exon 2
------tgatgtt--gctgaaatttcttctgtgtt-ctatcttttgtttgcatattgctatcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
|||| || |||| | | |||| | | ||||| ||| | || | | || | | ||| |||| | ||| | | ||||| | |||||||||| |||||| | ||||| ||||||||||| ||||| ||| |||| | || |||||||||||||||| || || || |||| ||||
tttactccatgtagggcccaaatagcataggtgtaattgtgggatgtttctataattcttctgtatgttat----gcaaattg---attgtttatgttgctt--gacagGCATCTGGTAACTCGAGTGCTTTATTCCTCACTGCTGCAGCACAAAACCTGTTGTGCTTGAAGCTAGCAGAGGAGCTTGGTGTAATCATTGCAAATCCAT
upper sequence: GLYMA15G06110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G64290.1 (Arabidopsis thaliana), 3'ss of exon 1
tgatgttgctgaaatttcttctgtgttctatcttttgtttgca----tattgctatcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
| || | | | | ||| | | | ||| ||| | ||| | | ||| || || ||| | | | | ||| || ||||||| || || ||||||||||| |||||| | |||||||||||||||||| ||||||||||||| ||||||||||||||||| || | | ||||||| |
---agatgaaagattctttcttgttgtttgtatttgacttgagagacttttgaagttttcgaattttgttctg-cttctctaattttgttctgatctttgacagTGCGCCGGAAACTCTAGTGCGCTTTTCTTGACTGCTGCAGCTCAAAATTTGCTGTGTCTCAAGTTAGCAGAGGAGCTTGGAGTAGTGATCTCAAACCCGT
upper sequence: GLYMA15G06110.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0017g00640.t01 (Vitis vinifera), 3'ss of exon 1
tgatgttgctgaaatttcttctgtgt-tctatcttttgtttgcatattgcta---tcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
||| | | | | | | | | | | | |||||| | ||||| | || | |||| | ||||| ||| | ||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||| || |||||| |||| ||||| ||||||| || ||| ||| |||||
-gatatgtttaataatatatatatatatattgtttttgtatatatatttttggcgccacatgataactacatgactatactcttgtgtgcatgat---tgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTGACTGCTGCAGCTCAAAACATGCTATGCCTCAAACTAGCTGAGGAAGTTGGGGTCATTGTTTCAAGCCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctatcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
atgtaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatgttgctgaaatttcttctgtgttctatcttttgtttgcatattgctatcatgtaataatgaagtgacttgtgcattgcctctgtgacctatgacagTCTGCTGGTAACTCTAGTGCTCTTTTCCTAACTGCTGCAGCTCAAAATCTGCTGTGTCTCAAATTAGCAGAGGAGCTTGGGGTGATAGTTCCAAACCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -tgttgct
- - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - tgctatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc