Sequence
atgc intronic sequence ATGC exonic sequence...agtcgcatcgcatgtccaccactgtggttgtcattgctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g50850.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G087472_T02 (Zea mays), 3'ss of exon 1
agtcgcatcgcatgtccaccactgtggttgtcattgctatgtactatttt-atcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
| | ||| | ||| || | || | | | ||||||| | | || | | | | | || |||||||| |||||||||| ||| ||||||| ||||||| || ||||| ||||||||||||||||| || |||||||||||||||||||||||||| | |||||||||||| | ||||||||| |
gttaatgttacatattcactacactttttctattaatattatactattctcacaatagttttaattaggt-tgctaatgacctggttctgcattttgatagGAAACTTTTGGTCGTTACCTCGACTTGCATGAGCTTTATAACGAGTTCATAAATTCCAAGTTTGGAACGCTAATGGAATACTCGACTTATGTTGGCTGTT
upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G010515_T01 (Zea mays), 3'ss of exon 1
agtcgcatcgcatgtccaccactgtggttgtcattgctat-gtactatttt-atcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
| ||| |||| | ||| || | || ||| ||| ||||||| | | || | | | | | || |||||||| |||||||||| ||| ||||||| |||||||| | ||||| ||||||||||||||||| || |||||||||||||||||||||||||| | ||||||||||| | ||||||||| |
gttaacattgcatattcactac-attttttctattaatattatactattctcacaatagttttaattaggt-tgctaatgacctggttctgcattttgatagGAAACTTTTGGCTGTTACCTCGACTTGCATGAGCTTTATAACGAGTTCATAAATTCCAAGTTTGGAACGCTGATGGAATACTCGACTTATGTTGGCTGTT
upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 3
agtcgcatcgcatgtccaccactgtggttgtcatt-gctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
| | | | || || || || | ||| ||| | | || | ||| || ||| | | ||| | |||||||||| ||| ||||||| |||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| | |||||||| ||||| ||||||||| |
atagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTACAAACAGTTTTAATTA-TGTTTTCTGATGAAGTGATGATCTGGTTCTGCATTTTGATAGGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT
upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 3
agtcgcatcgcatgtccaccactgtggttgtcatt-gctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
| | | | || || || || | ||| ||| | | || | ||| || ||| | | ||| | |||||||||| ||| ||||||| |||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| | |||||||| ||||| ||||||||| |
atagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTACAAACAGTTTTAATTA-TGTTTTCTGATGAAGTGATGATCTGGTTCTGCATTTTGATAGGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29664558|gb|CB660833.1|CB660833EST: GATTGTTTGATTCCTCTTGTAGGATCTCGGTGGTATACATG GAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATA
genomic: GATTGTTTGATTCCTCTTGTAGGATCTCGGTGGTATACATGgtaagattta ... aatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATA
EST:
gi|29664554|gb|CB660829.1|CB660829EST: GATTGTTTGATTCCTCTTGTAGGATCTCGGTGGTATACATG GAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATA
genomic: GATTGTTTGATTCCTCTTGTAGGATCTCGGTGGTATACATGgtaagattta ... aatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
tgctaat putative branch site (score: 2)
aatttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtcgcatcgcatgtccaccactgtggttgtcattgctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
- - - - - catgtcc
- - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttctgc