Sequence
atgc intronic sequence ATGC exonic sequence...ctaaaaagatagtagaccctatttttaattagaaaaactagttaaggaagctttttgttaaaggattttttgtctctcctaaagatatgtcgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
Basic information
species | Glycine max |
transcript | GLYMA02G45030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
ctaaaaagatagtagaccctatttttaattagaaaaactagttaaggaagctttttgttaaaggattttttgtctctc-ctaaagatatgtc--gtttgt-tagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
|| | ||||| | |||| || || | |||||| | |||| || | | || || ||| || || ||||||||||||||||| || ||||| |||||||| || ||||||||| | ||||| ||| |||| || | ||| ||||| | ||||||||||
-----gtcggggtttattatatttgtcccattaaaatttaatt--------tctttgttcta--atttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
ctaaaaagatagtagaccctatttttaattagaaaaactag---ttaaggaagctttttgttaaaggatttt-ttgtctctcctaaagatatgtcgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
| | | || | |||||| | | || || | || || | | | || | || || | || ||||||||| ||||||||||| || ||||| || || ||||||||||||||||| ||||| | | | || |||||| ||| ||||||||| ||||
--gtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------ctaaaaagata---gtagaccctatttttaattagaaa---aactagttaaggaagctttttgttaaagg-attttttgtctctcctaaagat-----atgtcgtttgtt-----agGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
|||| || || | | | ||| | || || | ||||| | |||| | || | |||| | | || | || || || | |||| ||||| ||||||||||| || |||||||| || ||||||||||| ||||||||||| | || ||||| |||| ||||| | |||||||| ||||
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------ctaaaaagatagtagaccct----atttttaattagaaaaactagttaaggaa-gctttttgttaaaggattttttgtctctcctaaagatatgt-cgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
|||| | | | | || | || || | ||| | | |||||| | | | |||| || || | ||| | ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| | ||||| |||||||||| | | ||||||||||
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagctttttgttaaaggattttttgtctctcctaaagatatgtcgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
tcctaaa putative branch site (score: 2)
ttaaaggatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaaaagatagtagaccctatttttaattagaaaaactagttaaggaagctttttgttaaaggattttttgtctctcctaaagatatgtcgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- aaaaaga
- - - - - - -agaccct
- - - - - - - - - - - - - - - agaaaaa