Sequence
atgc intronic sequence ATGC exonic sequence...catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattattgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55290.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G105827_T03 (Zea mays), 3'ss of exon 3
-catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattat-tgtt---cttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
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tagtttgtgtaggatgccttttgcaaatactcattt---tcctatggacaaattcaaa--ttgggtgtctgaaattacatgtcaaacttttatcatctcatgcagATTAAAGGTCTGTCTAATGTAAAGGAGGAAGTTTATGGAGCGCTTGACTCTTTTGTTGCATGGGAACTGGAGTTTCCCTTGATAGTAGTAAAGAAGGCAC
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G040970_T02 (Zea mays), 3'ss of exon 2
catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattat----tgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
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agtttatgtaggatgccttttgcaagtactaattttca-tatgggacac-attcaaa--ttgggtgtctgaaattatacaccaaacttttatcatcccgtgcagATTAAAGGTCTGTCTAATGTAAAGGAGGAAGTTTATGGGGCACTTGACTCATTTGTTGCATGGGAACTGGAGTTTCCCTTGATAGTAGTAAAGAAGGCAC
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G29590.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattattgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
|| | ||| | |||| | | | ||| |||| | | | | || | | | || || | || || | | | || || |||| | |||| ||||| || |||||||| ||||| ||||||||||| | |||||| |||||||| ||||| || || || |||| || ||||| |
gtaagtttttcctcattgcattccctctagtcgttcctgacattaatttaagcttcaattttgttttctctctgggaagttgtgacatt-ctcatttaattcagaaactttcggactgattttttct-tgggtgttttgcatttctagaaaagtaatttttctaatgtcttctacagATTAAGGAGCTGTCAAATGTCAAAGAGGAAGTTTATGGAGCTCTTGATTCCTATGTTGCTTGGGAATTAGAGTTCCCTTTAATTACAGTGAAAAAGGCTC
upper sequence: LOC_Os01g55290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G24100.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattattgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
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gtgagtttttccttattgcactccggctagtcattaatttaagcttcatttttgttttctctctgggaagttgtgacactctcatttaattcagaaacattcagactaattttttct-tggatgtttcacatttatggaaaagtaatttttctaatgtcttgtacagATTAAGGAACTGTCTAATGTCAAAGAGGAAGTTTATGGAGCTCTTGATTCCTATGTTGCTTGGGAATTAGAGTTCCCTTTAATTACAGTGAAAAAGGCACMapped 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|58695057|gb|CK083744.1|CK083744EST: CTCGCAAGAGAATCGGAACCGTTTCCAAGTCTCAAAAGCTTGTCGAATGT GTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCA
genomic: CTCGCAAGAGAATCGGAACCGTTTCCAAGTCTCAAAAGCTTGTCGAATGTgtgaggttct ... tttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCA
EST:
gi|58688529|gb|CK077216.1|CK077216EST: CTCGCAAGAGAATCGGAACCGTTTCCAAGTCTCAAAAGCTTGTCGAATGT GTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCA
genomic: CTCGCAAGAGAATCGGAACCGTTTCCAAGTCTCAAAAGCTTGTCGAATGTgtgaggttct ... tttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttattcatgcctcgagtacctgaaattattgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
ttattgttcttttgtc CT-rich tract
aaattattgttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttttgcatgacggattttgctgcaacagattcagactacctggtgttattcatgcctcgagtacctgaaattattgttcttttgtcctttcctgtagGTTAAAGGCTTGTCTAATGTAAAGGAGGAAGTATATGGTGCTCTTGATTCATTTGTTGCATGGGAATTGGAGTTTCCCTTGATAGCAGTAAAGAAGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG