Sequence
atgc intronic sequence ATGC exonic sequence...ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02150.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 7
-----------ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
|||| |||| || |||| | || | || |||||||| || || || || | ||||| | | || | ||| || |||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||| ||||||
ttggttctatgttggtgtgttgaaggaaa-acatac-------atgcacattggatggaaatggtccat--gttttcaactaagaataacattttattttcacat-cacagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGAGCTTTGTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 6
--ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgttt--ttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
| | || | || | |||| || | | || || || ||| ||| ||| | || | | | |||||| | | |||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||| ||||| ||||||
attttacatctttgattttatgttggcgtgtgaaggaaaccatgtatatgcatt----ggatggaaccatgtattcagctaagaataaaatttaattttcacagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGGGCTTTGTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
-----------------------------ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctc----caactgtttttcaagcttaa-attttctatatac---agGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
|| | | || | | | ||| | | |||| ||| | ||| ||||| | |||| | ||| | ||| |||| || ||||||||||||||||| || || ||||| |||||||||||| || ||| | | || ||||||
gtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------ctggtttgttcaaagaaatatatgcgtctgttgtggcc-------attggatttgtattttctatatgtctc----caactgtttttcaagcttaa--atttt--ctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
| | || | | ||| | | ||| | | ||| | | |||| ||| | ||| ||||| | |||| ||||| || || |||| || ||||||||||||||||| || || ||||| |||||||||||| |||||| | | || ||||||
gtttgtgaatttttcttttcatcaaatatatttctgtattggcttgggttttaggaagatttttgaatgctactcttacagcttgcttttattgagaaccaaaagtgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttaatgtagGTCAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCAAGAAGGTCATTGTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------ctggtttgttcaaagaaatatatgcg----tctgttgtggccattg-gatttgt---attttctatatgtctccaactgtttttcaagcttaaattttctata-tacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
|| | || || | | |||| | | || || || | | ||| | || ||||| | |||| | || || || | ||||||||||| |||||||||||||||| || || || || ||||||||||| | | ||| |||| | ||||||
gtttgtcttaactcggttaatacgttcaatattttttaatcacatccttttcccaatctcatgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttgccccagctttggtatgt-tgtggttgttggatacttatatatctttggcagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTTCCAACCATTGAAGATCCCAGTACCAGAAAAGCTCTCTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------------------------------------------ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatat----acagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
|| | | | ||||| | || || || || | | | | ||| || | | | | | | |||| || | | | |||||||||| |||||||||||||||| || ||||| || ||||||||||| | | ||| |||| | ||||||
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggc--ttggcccagc--tttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 6
-ctg-gtttgttcaaa-gaaatatatgcgtctg--ttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
||| | || ||||| ||| || | | ||| ||| | | | || | | || | |||||| || || || | | | || ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||| | | ||| || | | ||||||
actgtgctttttcaattgaattaaaggaaactggattgagattaaggatttctcactgactctga---cccaact--ttaacacttttgagccctatccattcagGTAAAGACCATGAGAGCTCTGCAGTACTTCCCGACTATTGAAGATCCAAACACTAGAAGATCACTGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtattttctatatgtctccaactgtttttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
ttttctat CT-rich tract
ttaaattttctatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - -aaagaaa
- - - - - - - - - - - - - -ctgttgt