Sequence
atgc intronic sequence ATGC exonic sequence...tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
Basic information
| species | Oryza sativa |
| transcript | LOC_Os05g42330.2 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
--tgcattgtctgctagcatttgtttctactgttgtagctaagatgccct-ttacaaagttgcttactatttatttacctaacttcacccttctct-tttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
| | || | || | | | || | || ||| | ||| | | || ||| | || | ||| | | | | ||| |||||||| |||| || ||||| ||||| ||||| ||||||||||| ||||| ||||| | ||||| ||||| |||||||| ||||||||||| ||||||||
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttata----tatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagtt-gcttactatttattt-----------acctaacttcacc--cttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
|| || ||| | || || | ||| | |||| | ||| | | || |||| ||||| || | ||| | ||||| | || ||||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||| | ||||| |||||||||||||| ||||||||||| ||||| ||
-------------agaatcagttgg-attggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G37590.1 (Glycine max), 3'ss of exon 3
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
| |||| | | | | || || ||| ||| | | | || ||| | ||| || |||||||||||||| ||||| || || ||||||||||||||||| |||| ||| ||||||| || | ||| ||||||| |||||||| ||||| ||| ||| |||||
--------------gtattt-tgagttcatctatacttacataaccca--acaggaataat-gcctttagtttggtggtttacacttttttcttttgcagCTGGAATTGTTATAGAGGATAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 3
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctc--ttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
| |||| | | || | | | || || ||| | | || ||| | ||| || | |||||||||||| ||||| || || || |||||||||||||| |||| ||| ||||||| || | ||| ||||||| |||||||| ||||| ||| ||| |||||
--------------gtattt-tgagttcttcaacactttacataacccaacaggagtaa--tgcctttagtttggtggtttacactttttttgtttttgcagCTGGAATTGTTATAGAGGAGAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
|| | ||||| || | | | || || || | ||| | | | | | | | ||| | || | ||| | ||| || ||||| || ||||| ||||| |||||||| ||||| |||||||| || ||| | ||||||||||||||||| || ||||| || ||||| || ||
-----------gtatc-tttgtcaatattatcttttgta-gaaacctgacatttcgttccatgtgaaatgctca--tgctgtcatctttat-tttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 5
tgcattgtctgctagcatttgtttctactgttgtagcta--agatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
| | | | | || || | | | | | | ||| | || | | | ||||| | || || | | | |||| ||||||| ||||| |||| || |||||||||||||| || ||||| | || || ||| ||||| | ||||| ||||| ||||||||||||| |||||||
-ctaataacattatggacttattcaatttcctcaaacctccaaacaccccattagtttttccatgcaatttacgt-ttcaagttttctactttgttttccagCTGGAATTGTTCTTGAGGAGAAAAATTGGCCACCATTCTTCCCAATTATCCATCATGATATTGCGAATGAAATACCGATTCATCTACAAAAGTTGCAGTA
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
||||||| | | | | | || || | || | || | || | | | | || | || ||| ||| ||||| |||||||| |||||||| || || |||||||||||||| |||||||| || ||||| ||| | ||| ||||||| ||||| || |||| ||| | |||||||
--gtttgtctgtt-gtttatatcattagtgaatcaattaggttgagtagtgt----tttcatgcagtctacaatctaaatatcattctt-tctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
acctaac putative branch site (score: 2)
cctaacttcacccttc CT-rich tract
ttactatttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
tgcattg
- - - - ctgctag
- - - - - - - - - -tgtttct
- - - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - gatgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctt
