Sequence
atgc intronic sequence ATGC exonic sequence...aaaaatgggatcgcatgttttttcttcgttacattttcagaaaattgatgtcgtctttcttccagcttaatttattgttctgtatacttcccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
Basic information
species | Glycine max |
transcript | GLYMA16G05570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26820.1 (Arabidopsis thaliana), 3'ss of exon 4
aaaaatgggatcgcatgttttttcttcgttac----attttcagaaaattgatgtcgtctttcttccagcttaatttattgttctgtatacttcccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
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----gtgcctttataacccccttgtaaagtaccaaaatggctatttaactgagaagatagctaatcccgtttaaacc-tttttgtgtgtgttt---------agACTTGGTGAAGCTTATTGAGAGGACAGTTAAGTCGGAGAACTACCGTTTCCCAAATAGACCAATATATTTAGTTGGAGAATCTATTGGAGCATGTCTTGC
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaaatgggatcgcatgttttttcttcgttacattttcagaaaatt---gatgtcgtctttcttccagcttaatttattgttctgtatacttc-ccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
|| |||| |||| | |||| | | | || | || | | |||| || || | | | | | ||||| | ||||| | |||| ||| | | |||||| | || | |||||||||||| |||||| | |||||||||||| | |||||||| |||||
----------------gtaccttct-cgttgccctttcgaagcactaccgagaagatagttaatgcgagttaaagccttattgtttgtgttctgttgtattcagACTTGGTGAAGCTTATTGAGGAAACCGTTAAGTCAGAGAACTTTCGTTTACCAAATAGACCAATATATTTAGTTGGAGAATCTATTGGAGCATGTCTTGC
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02030.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaaatgggatcgcatgttttttcttcgttacattttcagaaaattgatgtcgtctttcttccagcttaatttattgttctgta-tacttccca--cttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
|||| | | || || || | || | ||| | | | |||| || |||| | ||| ||| || || || | ||| | ||| | | | ||| ||||||| ||||| | ||||||||||||||||||||||||| | || || ||| ||||
------------------------------gtatttcc------tctatttcaactcttttagatctttttatctgattctctaacactttggatgcttttagATCTAGTCGCCATGGTTGAAACAACTGTCAAATATGAAAATCAACGATCACCTGGGAAACCCATATATCTTGTTGGAGAATCTCTCGGCGCCTGCATTGC
upper sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 3
aaaaatggg-atcgcatgttttttcttcgtt----acattttcagaaaattgatgtcgtctttcttccagcttaatttattgttctgtatacttcccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
| ||| | | || | | || | | ||| | || || | |||| | |||| | ||||| || | || | | | || | | | ||| | ||||| | | ||| |||||| || |||||| || | |||||||||| |||||||| ||||||||||||||| | |||| |||||||||
gatcatgcttactgtatttatcctcctaaatggggacaccataggacaagt-atgttgaatttcgtt----ttaatatagtcttttccaaattttcatcgttaagAATTGGTGAAGCTGGTTGAAAGAACAGTACGGTCAGAGAATTTCCATTCACCAAATAAGCCCATATACCTTGTTGGAGAATCTCTTGGAGGATGCCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgtcgtctttcttccagcttaatttattgttctgtatacttcccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
gcttaat putative branch site (score: 4)
cttcccactt putative PPT
ttaatttattgttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaatgggatcgcatgttttttcttcgttacattttcagaaaattgatgtcgtctttcttccagcttaatttattgttctgtatacttcccacttgcagACCTTGTGAAAATAGCTGAGAGAACAATAATGTCAGAACATCAACGCTCACCAAATAGACCCATATATCTTGTTGGAGAATCTTTAGGAGCATGCCTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta