Sequence
atgc intronic sequence ATGC exonic sequence...tgggggagacagtttaggtttcaagttttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
Basic information
species | Glycine max |
transcript | GLYMA03G40980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 2
tgggggagacagtttaggtttcaagt---tttaagctttctat-cttataagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgc--agTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
| | || || | |||| | | || ||| | | | | | | | | || | || || |||| || | ||| || | | | | | ||| ||||| || ||||| || ||| | || || | || |||||| |||||||||||||||||||| ||||||| ||| | ||||||||||| || ||||
-gtatgtttcaattaacatttccattctattaaagtatgttgttcctccatttcatttcatttttg-ttcattgttt-taaatgtttttttttttggttttcccagTCGTTTATCTCGATGCTGATACTGTGGTCGTGAAAAGTATTGAGGATCTTTTCAAGTGTGGGAAGTTCTGTGGCAACCTGAAGCATTCTGAAAGAATGAA
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
-tgggggagacagtttaggtttcaagttttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgc--gttgaatg-tgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
| | ||||| | |||| |||| | | | | ||| | | | | | | | || ||| || | | | ||||| || | | |||||||||||||||| || || ||||| || || | || ||| || ||||||||||||||||| || || |||| ||||| ||||||||||| || ||||
gtatgcttttcagtt-atttttctagttcatcgttatatgtctc-tgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
-----tgggggagacagtttaggtttcaagt-tttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
| | | | | || || || ||| || | | | | || || | |||||| || |||| || | | | | ||||||||| || |||||||| ||||||||||| |||| || |||||| ||||| || || || ||||||||||||||||| || ||||||||||||||| ||||
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatc-tagaagaacagttttatttagtgattat-tgt----tattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
ttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggggagacagtttaggtttcaagttttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-gggggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt