Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
Basic information
species | Glycine max |
transcript | GLYMA17G00480.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
| ||| || || | || || ||| || |||||| | | | | || || || | || |||||||||| ||||| ||||| |||||||| ||| |||| ||||||||||||||||| | ||||||||| ||||| || |||||| |||| ||||||||||
-----------------------gtaaattcaaaagcccttctagaattaattttagagtgggcacactttgcttatgatgattactgttatctttata--ttctagATTGTCCTGGAAGCCGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGTTTAAAATCCTTAATAAAAGGAGTACTTGAAATGGCAAAGGAGCCAT
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
|||| | || | ||| | || || | | || | | || | | ||||| | | | || | ||||| |||||||| | ||||| ||||| |||||||| || ||||| |||||||||||||| ||||| ||||| || || || | || |||| ||||||||||
gtaagattggatcc---agtttcaggattagtgctactatcaggcattttcccatcttttatgaacact-gaacagtattctctgacattct-------------agATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctg-ttgacacttggggtgcttgcttctatat-tctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
||| | | | | ||| | | ||| |||| ||| || || | | || || | | | || | |||||||| | ||||||||||| |||||||| ||| |||| |||||||||||||| |||||||||||||| ||| || || ||| |||| ||||||||||
-------------------------gtat-gatcacttccaattt--tacattgagctctggttggcagttag--cacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
|| | | || | ||| ||||| || | | | | | ||| ||| ||| | | | ||| || ||| |||||||| || | || || ||||| |||||||||||||| || |||||||||||||| |||||||| ||||| ||| ||||||||| |||| || || |||
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctt-----------tagac---tggagtg-tgacagattgattttccaattg--tttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
|| | | || | |||| || |||| | | | | | | |||| ||||| ||| |||| |||| |||||| |||| | || |||||||| |||||||||||||| || |||||||||||||| |||||||| || || || || ||||| |||| || || ||
gtgggtgtcttct------tctgtcctaa-gtttctgcacgagacaagtt-----------ttgagacttga----tttgtcaaaatatc-----tttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgct-tctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
||| ||||| || ||| | || || | || | || || || | | | | || |||| | | || ||| || | | |||||||| |||||||||||||| |||||||||||||| || |||||||| |||||||| || || |||| ||| || || || |||||||| |||||||
gtatgg-ttctctttt--attcacattccaacttttgtgccttttaaat-atgttgttgta---aggcctttattgtttgcaatgttccttttcaatt--gataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
tgttgac putative branch site (score: 3)
ttctcatttt putative PPT
tatattctcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG