Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
Basic information
species | Glycine max |
transcript | GLYMA09G37610.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
-------gta-tgttcttttccttttttaacttaaatt-agttaagcatcttgttctttgctatttac-tcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
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gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
--------------gtatgttcttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgtttt----ggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
|| | | | ||| | ||| | ||| || || | ||| | | | | | |||||| | |||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||||| |||||||| || || |||||||||
gtatgttgtagcatataatcacctgttcttcctatccttctctctgtttag--tcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
------------gtatgttc--ttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
|||| || | |||| | |||||| | ||| || | | | | | | | | | | ||| ||||||||||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||| ||||||| |||||||| ||||||||||| ||| |||||||||
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgtt---cacccaggccctgagttctgtttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 12
-------gtatgttcttttccttttttaacttaaattag--ttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
||||| | | | ||| || |||||||||| | | | | | || ||| | | || | ||| |||||||||||||| |||||||||||||||||||| | ||||| || ||||| || || | || | ||||| ||||||||||| || | |||||| |||||
gtaagatctatgt-catcccatttctttacttaaattaagatgtaacctttctctcccagcttagttgtgttttatttgggcagTGGTGATAGGACTCCCAAACAGAAGGTGAAATTGAAAGTCACAGAGGAGAAGCTATTGAATTTGATGTTAAAATACAATGGGGGGAGGCCTAGATCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttaaattagttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
ttttaac putative branch site (score: 2)
tttactcttctgtttt putative PPT
aaattagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA