Sequence
atgc intronic sequence ATGC exonic sequence...cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os09g32680.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G408242_T01 (Zea mays), 3'ss of exon 1
cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
| | | ||| || ||| || ||| ||| | | | || | | |||| |||||| | | | || |||| ||| ||||||||| | || |||||||||||| |||| ||||| || ||||||||||||||||| |||
ctgaaaaacattgaattatttgttctagtggggccttgaattttttgtatgtgtatattttgtagtgagaactttgttttaacacaaaattcgtttccagGAAGAGCATGTCAGACTATGATCCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAG------------------------------------
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 4
cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
| | | ||| || ||| || ||| ||| | | | || | | |||| |||||| | | | || |||| ||| ||||||||| | || |||||||||||| |||| ||||| || ||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||
ctgaaaaacattgaattatttgttctagtggggccttgaattttttgtatgtgtatattttgtagtgagaactttgttttaacacaaaattcgtttccagGAAGAGCATGTCAGACTATGATCCTCGTTTGGTTGCACCTACTTGTTTGTATTTGGCATCTAAGGTGGAGGAGAGTACAGTGCAAGCCCGACTTCTTGTA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
cacagtgctttctaatatttcattccagaacatttaat---tctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
| | | || ||| | | | | | ||| | || | | | | | | | |||| | | | | | | | | | ||| || ||||| ||||||||||||||||| ||| ||||||| ||||| || ||||| |||||||||| | ||||| ||||||||||| || | ||||||||
-ataatactatcttct-tctgaccctggaagttgtagtatatgcctaataaacttccttaacaag-tgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 5
-cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
| | | ||| | | | | | | || | | | | | |||| | | | | | | | | | ||| || ||||| ||| ||||||||||||| || ||||||| ||||| || ||||| |||||||||| | ||||| ||||||||||| || | ||||||||
ttatactatcttcgtctgaccctgaacgtagtagtatatgcctaataaacttcccttaacaag-tgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGGCTGAATATGATCCACGCTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTAMapped 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|88306627|gb|CI671386.1|CI671386EST: GGTGATAGCTACTGCTGTTACTTATTTCAGGCGTGTATACACAAG AAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTA
genomic: GGTGATAGCTACTGCTGTTACTTATTTCAGGCGTGTATACACAAGgtatgattct ... atgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
ttctgat putative branch site (score: 3)
tattagaattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacagtgctttctaatatttcattccagaacatttaattctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA