Sequence
atgc intronic sequence ATGC exonic sequence...ttctctcttttatgctctttgaattattggtttttccttgtacttcttttgcatgtatacttgggattagtgaaataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
Basic information
species | Glycine max |
transcript | GLYMA06G43820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 5
ttctctcttttatgctctttgaattattggtttttccttgtacttcttttgcatgtatacttgggattagtgaa---ataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
| | || || || |||| || | || || | | | | |||| | ||| | | | | | || ||||| | | |||||||| ||||||||| ||||| ||||| || ||||| |||||||||| || ||||||||||| |||||||||||||| || ||||| | ||||
--caccctagaatttatcttaaatttacctcttctgaagatatttatgtaaggt-tgtactggtaattcttaagcggagccagtaattcatagtcttctacagGTTTCCATGATGGAACGCGATTTTTATCTAGGACGAATACTGACTGGACGAGTAAGATCTGGGGTTGTCCGTGTTGGTGACAAAGTGCATGGTCTTCGTA
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 5
-ttctctcttttatgctctttgaattattggtttttccttgtacttcttttgcatgtatacttgggattagtgaaataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
||| | | | || ||| ||| | | || | | || ||| | | || || | | || | || ||| ||||||||||||||||| || || |||||||| || ||||| || |||||| | || ||||| ||||| ||||||||||||| || ||||| |||| |
attcatttatacgtaactattattttaagggtataaaatgtctgaactgctaaagccctagcaatgat-atttaactatcgttctctcttctgatttccagGTTTCAATGATGGAGAAGGACTTCTATCTCGGACGAATATTAACTGGAAGAGTAACTTCTGGAGTTGTCCGTGTTGGTGACAGAGTCAATGGACTACGCA
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 5
-----ttctctcttttatgctctttgaattattggtttttccttgtacttcttttgcatgtatacttgggattagtgaaataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
||||||| | | | | || |||||| | ||| | || | || |||||| | || || | || || | ||| ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| | | ||||| ||| | |||||||| |||| || |||||| | ||||
cacttcctcctctttttcagtttctttactacctttttttcttcaagcttttctta----tttaattgggaacattggaaaat-atatttgacagtttatttcagGTTTCCATGATGGAAAAAGATTTTTATCTTGGGCGAATATTGACTGGACGTGTTTCTTCTGGTGTTATCCGTGTTGGGGACAGAGTACATGGACTTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgcatgtatacttgggattagtgaaataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
gcttaat putative branch site (score: 4)
tgcttttc putative PPT
ttaatagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctcttttatgctctttgaattattggtttttccttgtacttcttttgcatgtatacttgggattagtgaaataccatgcttaatagtgcttttcagGTTTCAATGATGGAAAAAGATTTCTATCTTGGGCGAATTTTGACTGGACGCATATTCTCTGGGGTTGTTCGTGTTGGTGACAAGGTTCATGGATTACGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - tatgctc
- - - - - - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgct