Sequence
atgc intronic sequence ATGC exonic sequence...attttttctgattctggaaatctactcttctattgctactagttacttctactgtcttgatcttttttagttcataaagtcatagcctccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
Basic information
species | Glycine max |
transcript | GLYMA06G03040.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 6
-----attttttctgattctggaaatctactcttctattgctactagttacttctactgtcttgatcttttttagttcataaagtcatagcctccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
||| ||| ||||| || ||| | | | | | | |||| | ||| || |||| | || | | || |||| | | |||||||| ||||||||||| ||||| || ||||||| |||||||||||||||||||||||||| |||||||| || |||||||||||||||
gccaggactttcttgaacatggaaggctgatctggttagaaaagaaatatacttttctgtgt--atccattggagttgac---ttcgaacttataaatattgcagGCTGAGAAAAATGTTTTTGTTGTCTTCTATTCCGGGGAAAGAGCGAAAAGCAAAATTCTGAAAATATGTGAAGCTTTTGGGGCCAATCGTTATCCTTTCA
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
---attttttctgattctggaaatctactcttctattgctactagt-tacttctactgtcttgatcttttttagttcataaagtcatagcct---ccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
|| |||||| ||||| || | ||| | | | | |||| | |||| | |||| ||| || | | | || | | ||||||| | | |||||||||||||| ||||| |||||||| ||||||| |||||||||||||| || |||||||| |||||||| || ||||| |||||||||
aagatattttcta--catggaatcctggt--tctgtcagaaaaaatatactcattctgttt--gcctttgctagga-attgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 6
attttttctgattctggaaatctactcttctattgctactagttacttct-actgt--cttgatctttttta-gttcataaagtcatagcctccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
||||| | | || | ||| | | | | | || || | | || ||| |||| | | || | | | || || |||||||| || | |||||||| |||||| | || | |||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||| || ||
-ctttttatagggttataacacagttctcttttagtttcatcttcctcttgattgatgcttcatctcactcatgtgtactagttttaagagtc---ttttacagATTGAGAAAAATGTGTTTGTTATTTTCTTCTCTGGAGAAAGAGTGAAGAACAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTACCCGTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctactgtcttgatcttttttagttcataaagtcatagcctccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
tcttgat putative branch site (score: 4)
cctccctttttac putative PPT
ttttttagttcataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttttctgattctggaaatctactcttctattgctactagttacttctactgtcttgatcttttttagttcataaagtcatagcctccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - -gattctg
- - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - -tctactg