Sequence
atgc intronic sequence ATGC exonic sequence...cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g47500.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 9
cacgatatatttgtgcattctctttcctttcatccttatggatgtgac-agtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
|| | || ||| || | || | || | | | | || || | | || ||| | || ||||| | ||||||||| ||||| ||||| |||| |||||| ||||||||||||||||| | ||||| | ||||| || || |||||| | ||||
----------------gttagccttacttgcaactttgtcaattccattaatgaaattatgcattatggacatcatgagaatattttgtctgctg-tgtagGCAAAGTATGAAGAGGCAAGTCAAGTGGCAAATGATGCTGTTGGTAGCATCAGAACCATTGCATCATTCTGTGCCGAATCAAAGGTGATGGATATGTACA
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 9
--cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
|| |||| || || |||| ||| || || || ||| | | | |||| ||| ||| | ||| | ||| | |||||||| || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| | ||||||||| || |||||| || ||||
gttggtctaaatttagttatgctgattcc----atcaatagaaattagaaagtaagcat--atgttgacaagagtcc-tttgtcttt----------tatagGTGATGTATGAGGAGGCAAGTCAGGTGGCAACTGATGCTGTTGGTAGCATTAGAACTGTTGCATCATTCTGTGCTGAGCCAAAGGTGATGGAAATGTACA
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
||| || | || | ||| || || || | | || | | | | | ||| | | ||| | | || | ||| |||||||||||||| || ||||| || | ||||||||| | ||||| ||||| || ||||||| ||||| ||| ||||||||||| ||||
--------gttttaatatagtggttacaa-catttttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtt-tagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
-cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
| | | | | ||| | | ||||||| || ||| | ||| ||| | | | | || | | | | ||| | ||||||||||||||||| |||||||||| |||||||||||| ||||||||||| || ||||| | |||||| || ||||| |||||| | ||
gttggtaacactcctcacttcccggttatttcatcatt-------tgaaatgaattcttagattcactaaggccc--------ttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 11
cacgatatatttgt-gcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
| || |||||| || | | || | | ||| | | | || ||| || || || | || | ||||| | ||||||||||||||||| |||||||||| |||||||||| | ||||||||||| || ||||| | ||||||||||||||| |||||| | ||
--------gtcagtagcattccctgtgagtatatgttctgcattatgaaa--------tgacgt-gttgattcattgaagatattataaatttt-ttgtagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTAGCAGCATCAGAACGGTTGCATCATTTTGTGCTGAGAAGAAGGTGATGGAGATGTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
gtttgat putative branch site (score: 5)
atttttaaagttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -tgcattc
- - - - - - - - - - - - - - ttcatcc
- - - - - - - - - - - - - - - - - - -atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga