Sequence
atgc intronic sequence ATGC exonic sequence...agcattgcagtaatgccatggttctacatttatttggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g37590.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G168614_T03 (Zea mays), 3'ss of exon 4
agcattgcagtaatgccatg-gttctac--atttatttggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG-----------
| | ||| || || ||||| | | | | | | | | || || |||| ||| ||| || || || ||||| | ||||||||||||||||||| || |||||||| || || ||||| || |||||||||||| || ||||||||| |||||||||||||||||||||
--cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctat-agacgaattataacccctgctgctctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAGGTATGCGATAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G168614_T02 (Zea mays), 3'ss of exon 4
agcattgcagtaatgccatg-gttctac--atttatttggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| | ||| || || ||||| | | | | | | | | || || |||| ||| ||| || || || ||||| | ||||||||||||||||||| || |||||||| || || ||||| || |||||||||||| || ||||||||| |||||||||||||||||||||
--cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctat-agacgaattataacccctgctgctctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
agcattgcagtaatgccatggttctacatttatttggaac-tcttaagtagttatgttttttttccatatt-agatatatcatgacatctgct-tatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| ||| | || || || || || | | | | | || | | |||| ||| || | | | | | | ||||| |||||||||| || |||||| |||| ||||| || ||||||||||| || |||||||| | |||||||||||| || ||||
---gcaaccaacatgaatttattaataatgtacctgaaatatgtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 3
agcattgcagtaatgccatggttctacatttatt-tggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| || | | || | | | | || | | | | || || | | | | || | || | | ||||| | | |||| ||||||||||| ||||| || ||||| ||||| || ||||| ||||| ||||||||||| |||||||||||||||| || ||
aagatagagaacactgcagtatatgataactgttgttggattgcaaactatctccatactctgctattaatgccaatctttgggtttctgca-actggcagATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G02010.1 (Glycine max), 3'ss of exon 4
--agcattgcagtaatgccatggttctacatttatttggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| || | | | ||| | | | | | ||| | || || | | | || | || | ||||| | || |||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||||||||||| ||
tcaagatag-aacactgcagtatatgataactgtcgttgaattgcaaactatctgcatactcggctattaatgccaatctttctgtttctgcat-ttggcagATTACGGATGCTGTTGTTGCTGCACGAATTTTGAATGCTACTCTTGTGGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGATTCTAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA14G00520.1 (Glycine max), 3'ss of exon 3
agcattgcagtaatgccatggttctacatttatttggaactcttaagtagttatgttttttttccatattaga---tatatcatgacatctgcttatt--tctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| | || || | || | | ||| | | | ||| | ||| | || | ||| | ||||| | |||||||||||||||| || |||||| |||| ||||| || ||||||||||| || |||||||| | |||||||||||||| | ||
-----tctggcggggctatcagacaccaatataataagtgatttagggatacaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
upper sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 4
agcattgcagtaatgccatggttctacattta---tttggaactcttaagta----gttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
| | || | | ||| ||| ||| | ||| | || | | ||| ||| || || | | | ||| |||| |||| ||||| |||||||||||||||||| |||||||||||||| || ||||| ||||| || ||||||| | || || |||| ||| | ||
---actatggtgctattgttgttttaccttttagttacagaattttttatcatattattaaatttgttgctcaggctgagcttgtt---acacctgcc-attttcagATAACTGATGCTGTTGTCGCTGCCCGCATTTTAAATGCTACTCTTGTCGTTCCAAAACTGGATCAGAAGTCCTTTTGGAGGGATGCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
cttatttct CT-rich tract
ttatgttttttttcca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcattgcagtaatgccatggttctacatttatttggaactcttaagtagttatgttttttttccatattagatatatcatgacatctgcttatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
- cattgca
- - - - - - - gccatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgc