Sequence
atgc intronic sequence ATGC exonic sequencegtttgtagatcaggcattgccaatattctcgagttaactcttttttatagattttgtatgtattaacactgtttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
Basic information
species | Glycine max |
transcript | GLYMA08G24290.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
gtttgtagatcaggcattgccaatattctcgagttaact--cttttttatagattttgtatg-tattaacactgtttatttgggttaaat------cagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
|| | | || || | || | || | || | || | | ||| | | || | || ||| || | ||| ||| | ||||| ||||| | ||| |||| || || |||||||| || | || |||||||| | ||||||||||| |||||||| ||||||||||||
----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 15
----------------------gtttgtagatcaggcattgccaatattctcgagttaactcttttttatagattttg-tatgtattaacactgtttatt-tgggttaaat-cagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
| | || | | | || | | | | || | | | | | | | | | | | || ||| ||| | ||||| ||||| || ||| ||||||| ||||||||||| ||| | || |||||||||| || ||||||||||||||||| || ||||| ||
gtttgtccacgccctccatcccatctcatcctcttgtgtctctgcggtttactactcagtgtagcattgccatctgcgatgtaacctgatcccgcctgtggtaaactatgcacagGGATCTGAAGGAGCATCTCAGAAGGTTGCAGCAGCAGTCTGATTCCCGGAGGAGGGCTGCTGTGAATGAGATGATGAGGCAGAGAGCGGCGGAAGTGGCC
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
---------gtttgt-agatcaggcattgccaatattctcgagttaactctttttta------tagattttgtatgtattaacactgt------ttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
| | | || | | | ||| || | | | | ||| | |||||||| | || | || ||| | | | | |||| || ||||||| ||||| || || | ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || ||||| |||||||| |||
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 16
gtttg--tagatcaggcattgccaatattctcgagttaactcttttttatagattttgtatgtatta---acactgtttatttggg------ttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
|||| || || || | ||| | | || ||||| | | | | || | || | | || | ||| | || |||| || ||||||||||||| || ||| | || || || || ||||| |||| |||||||| || ||||| |||||||| |||||||| |||||||| |||
-tttggatatattagaaccggggcataacatatggcaaagcttttttgaaaaaaatggtccgcatgatttgtattgatcattgtaaatcttctcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAATCAGATTCTAGGCGGAGAGCTGCCGTCATGGAGATGATGAGACAGAGAGCTGCAGAAGTCGCT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
gtttgtagatcaggcattgccaatattctcgagttaactcttttttatagattttgtatgtat-taacactgtttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
|||||||| | ||| | | | |||| | || | ||| || | || || | | ||||| | | | |||||||| | ||||| ||| | |||||||||||||| ||||||||||| |||| ||||||||||||||||| |||||||| |||||||| ||||| ||||||
gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactcttttttatagattttgtatgtattaacactgtttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
tattaac putative branch site (score: 1)
ttttttatagattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtagatcaggcattgccaatattctcgagttaactcttttttatagattttgtatgtattaacactgtttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT