Sequence
atgc intronic sequence ATGC exonic sequence...caagcagggtgaactaattaggaacagacatgccacagtactgatctcttttacttttctttgtgcaatacttactctctatgttttctcttgttgacagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
Basic information
species | Glycine max |
transcript | GLYMA09G08270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 2
caagcagggtgaactaattagg--aacag-acatgccacagtactgatctcttttacttttctttgtgcaatacttactctctatgttttctcttgttga---cagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
| | |||| || || || || | | | | | || | ||| | ||| | | | | | | | | | || |||| ||||||||| ||| || || ||||||||||| ||||||| ||||||||||| ||||| || |||||||| || || ||||| || |||||| ||||
------gactcaacttatgtggctaatagtattttctttctttgccaaacctgggagtttaatctgtcaactgtatgattgatggctaattgatgatggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATCGCCAAAAGCTGCTTAACCACACGAGAGGACCACTGGTGCAGATAATGTG
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 2
caagcagggtgaactaattaggaacagacatgccacagtactgatc-tcttttacttttctttgtgcaatactt------actctctatgttttctcttgttgacagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
|| || | | | ||| || || |||| | |||| | || ||| || |||| | ||| | ||| || || ||||| |||||||||||||||||||||||||| ||||| ||||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||||||| ||||
------ggttgtagccacgctggacac-tataccttcatactttttgtcttgaagattacttcgttgctgactttgtctgattctatctgtcatcactgaccaacagGGCATAATGGTACCATAAATGGACAGGGCCAAACTTGGTGGAAGAAGTATCGCCAAAAGCTTCTCAACCACACTAGGGGTCCACTTGTTCAGATAATGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttttacttttctttgtgcaatacttactctctatgttttctcttgttgacagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
tacttac putative branch site (score: 1)
cttactctctatgttt CT-rich tract
ttactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagcagggtgaactaattaggaacagacatgccacagtactgatctcttttacttttctttgtgcaatacttactctctatgttttctcttgttgacagGCCATAATGGTACCATAAATGGACAGGGACAAACATGGTGGACAAAGTATCGCCAGAAGCTTCTGAACCACACAAGGGGGCCACTTGTTCAGATATTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - gggtgaa
- - - - - - - - - - - - - - catgcca