Sequence
atgc intronic sequence ATGC exonic sequence...caacttttcaggttaactgaacgtatcataaatgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaattattattatcatttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g15660.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g15660.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G119749_T02 (Zea mays), 3'ss of exon 4
caacttttcaggttaactgaacgtatcataa-atgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaa----ttattattatcatttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
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---gagtcgagggtaat--aacaaatcatgctatgtgcagtgcaccatataagagattttccttagaaaactactctgtaacgctttacgctttcttacttgcagGTGTGTATGGTGATTGTGGTGGTGTATTGGTTGATGAGGA------------------------------------------------------------
upper sequence: LOC_Os01g15660.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G119749_T04 (Zea mays), 3'ss of exon 4
caacttttcaggttaactgaacgtatcataa-atgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaa----ttattattatcatttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCT-TTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
| ||| ||| ||| ||||| ||||||| | | || | ||||| | | || ||||| ||| || || ||||||||||||||||||||||||||| || ||||||||||||||||| | | |||| | | || | || | ||||| ||||||| || |
---gagtcgagggtaat--aacaaatcatgctatgtgcagtgcaccatataagagattttccttagaaaactactctgtaacgctttacgctttcttacttgcagGTGTGTATGGTGATTGTGGTGGTGTATTGGTTGATGAGGAGTAAGGGACTCGTTGGTTCTTTTCTCGTCCATGAAGTACAT-TTTAATAGAAAGCTAAATA
upper sequence: LOC_Os01g15660.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G19690.1 (Arabidopsis thaliana), 3'ss of exon 4
caacttttcaggttaactgaacgtatcataaatgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaattattattatcatt--tttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
| ||| | |||||| | || | | ||| ||| || | ||| ||||| ||| || | | | || ||||||||||||| |||||||||||||| ||||| |||| |
gtattttcctttttaactttcctcattacatcaatgc-------ttctg-----cttccacagtagacaggaacttacaatacttctctttgatgcttgcagGTGTGTATGGAGATTGTGGTGGTGCGTGGGTCAATGAAAA------------------------------------------------------------Mapped 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|29642826|gb|CB647833.1|CB647833EST: GACTGGGATTCCTCCCTGGACTTGTGAACTGACCCCTGCATTGCACCAAG GTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGT
genomic: GACTGGGATTCCTCCCTGGACTTGTGAACTGACCCCTGCATTGCACCAAGgtgtgagtaa ... catttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGT
EST:
gi|88387569|gb|CI583087.1|CI583087EST: GACTGGGATTCCTCCCTGGACTTGTGAACTGACCCCTGCATTGCACCAAG GTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGT
genomic: GACTGGGATTCCTCCCTGGACTTGTGAACTGACCCCTGCATTGCACCAAGgtgtgagtaa ... catttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgaaaaatttttctgccatacaataacttgtaattattattatcatttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
caataac putative branch site (score: 2)
tcatttttc putative PPT
atacaataacttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacttttcaggttaactgaacgtatcataaatgtgcaaactagccctgaaaaatttttctgccatacaataacttgtaattattattatcatttttcagGTGTGTATGGTGATTGTGGTGGTGCATGGGTTGATGAGGAGTAAGATAAGTGGCTTTCTGTAAGTGCTTCTGCAATAATTGTTTAACTGAAAGCTGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA