Sequence
atgc intronic sequence ATGC exonic sequence...agtattcattcttattcttggtattacatgtgatataggatacatggcaggcacatttttaatttttttaattaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
Basic information
species | Glycine max |
transcript | GLYMA13G11390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 5
agtattcattcttattcttggtattacatgtgatataggatacatggc-aggcacatttttaatttttttaa---ttaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
| || || | ||| || | ||| |||||| | || ||| | | ||| || || | ||| || ||| | | | | ||||||||||||||||| ||||| |||||||||||||||| ||| |||| || || ||| | |||||||||| ||| || || || | |||
-atgtttgcctttttctttgaagtttgac-caatacca-atacattttgatacatctttgtgtgtctttcaaattttgagagtagatttttcttct-tctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG
upper sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------------------------agtattcattcttattcttggtattacatgtgatataggatacatggcaggcacatttttaatttttttaattaatagtt-tatctttatgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
|| || | | | || | | | | || | | ||||||| || ||| ||| ||| || | ||||| || | | |||||||||| |||||||||||||| |||||||| || || | || | |||||| ||| ||||||| ||| ||| || || || || |||
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgta---tttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAG
upper sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------------------------agtattcattcttattcttggtattacatgtgatataggatacatggcaggcacatttttaatttttttaattaatagtt-tatctttatgatat-attcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG----
|| || | | | || | | | | || | | ||||||| || ||| ||| ||| || | ||||| || | | |||||||||| |||||||||||||| |||||||| || || | || | |||||| ||| ||||||| ||| ||| || || || || |||
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgta---tttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA
upper sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
agtattcat-tcttattcttggtattacatgtgatataggatac-atggcaggcacatttttaatttttttaattaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
| |||| || | | |||||| | | | || ||| || || ||| ||| | ||| ||| | | | || | |||||||||| ||||| ||||||||||| |||||||||||| || || | |||||||| || ||||||||||||||||||||||| || | |||
aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcc--tttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcaggcacatttttaatttttttaattaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
aattaat putative branch site (score: 3)
atttttaattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtattcattcttattcttggtattacatgtgatataggatacatggcaggcacatttttaatttttttaattaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG
- - ttcattc
- - - - - - - - - - - - -acatgtg
- - - - - - - - - - - - - - - - - - - - - catggca