Sequence
atgc intronic sequence ATGC exonic sequence...tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
Basic information
species | Glycine max |
transcript | GLYMA02G05470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05470.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 2
tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
| ||| | || || || | ||| || || | ||| | | | ||| | || | || |||||||||||| |||||| ||||||||||| || |||||||| |||||||||||||| | |||| |||| || || ||||| || ||||| || ||
-----------------gtgagtac-tacggccacactgtatccttggtgatt--ttgttttagatcatgcatctctt---aggcaatgtgaacttgcagTATCTGAGCAATGGGAGGTTCAAGAACGCGGATCACCAGGCGGTGGTGAACTCCGACTGCTGCCGGCTGTCGATCGCGACGTTCCAGAACCCGGCGCCGG
upper sequence: GLYMA02G05470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
|| | || |||| || | | | || | || | ||| | ||| ||| | || | || | ||| ||| | ||| |||||| |||||||||||||||||||| || || ||||||||||| || ||| | || |||||||||||||| || ||||| || ||
----------gttagtactctatccattta-ttggcttttttgtttctctgtttttggttttgacttggtcaatcttgatt------tgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
upper sequence: GLYMA02G05470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g14310.t01 (Vitis vinifera), 3'ss of exon 2
tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttca------taatttaaatttgttcattt-ttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
||| | || | ||| | || | | | || || | ||| | || ||| | || | | | | | ||||||||||| |||||| |||||||| ||||| || |||||||| ||||||||||| | || || ||||| || |||||||| || |||||||| |||
---------gtga-gtagtgattctctgcttattcctcttttggattccccatcgaaggggcagaataatataattaattaactctgcattcgattgacgtgggcagTATCTGAGCAATGGGAGGTTCAAAAATGCGGACCACCAAGCTGTGGTGAACTCCGACTGCAGTCGGTTGTCGATTGCCACGTTCCAGAACCCAGCCCCAG
upper sequence: GLYMA02G05470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 2
tttatttttatgaa--gcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
| | | | | | || | || || | || | | || | | | | | | | || |||| | | ||| |||||||||||| |||||| |||||||||||||||||||||||||||||||||||||| ||||||||| | |||||||||| || || |||||||| |||||
tatgtggtcaacatccacaatagtccttcctgatatggtattcaaattcatgctacccgaacccgaaagagagagtgattattggtttg-gtatgg-tgcagTATCTGAGCAATGGGAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCCAATCATAGCAGACTGTCCATAGCAACATTCCAAAACCCCGCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
tttcataatttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatttttatgaagcagcaagtctatttggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcatgaatgcagTATCTGACCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAATCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCAGCACCAA
- - - - - - -agcagca
- - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - -cgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggg