Sequence
atgc intronic sequence ATGC exonic sequenceCTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaattacttctgttctacttttacacagctatgaattactaaaaaaatgtt...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g44400.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G022866_T01 (Zea mays), 5'ss of exon 5
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaattacttctgttctactttta-cacagctatgaattactaaaaaaatgtt
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CTTGGACCTAGATGTATTATTTTACCCCTGTCCTAAAAAAGGCCCAACATTCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagacg-tcctacataaattctgatattctattctgtgttagcacttcagatcatatttggttgctagcatctccacatccacatccacgtatgtt
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G825090_T03 (Zea mays), 5'ss of exon 5
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaatt-acttctgttctacttttacacagctatgaattactaa--aaaaatgtt
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CTTGGACCTAGATGTATTATTTTACCCCTGTCCTCAAAAAGGCCCAACATTCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagacg-tcctacataaattct--gatattctattttgtgttagcacttcagatcatatttggttgctagcatctcctcatccacatccacgtatgtt
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G085000_T03 (Zea mays), 5'ss of exon 4
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaattacttctgttctacttttacacagctatgaattactaaaaaaatgtt---------
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CTTGGACCTAGATGTACTATTTTACCCCTGTCCTCGAAAAGGCCCAACATTCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaa-ccatcctacataagttcctta---cctaaagtcattcggttgatagcgcccccacagc-----catgtctatgaaatacggaaatgtggcgtatgaatta
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G825090_T05 (Zea mays), 5'ss of exon 5
-CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaatt-acttctgttctacttttacacagctatgaattactaa--aaaaatgtt
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TCTTGGACCTAGATGTATTATTTTACCCCTGTCCTCAAAA-GGCCCAACGTTCCGACCTAAAGTCCTCGAAATGGGTGGAAAGAAACAATTCCCTTACATGgtatgcagacg-tcctacataaattct--gatattctattttgtgttagcacttcagatcatatttggttgctagcatctcctcatccacatccacgtatgtt
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G22160.1 (Glycine max), 5'ss of exon 5
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaattac---ttctgttctacttttacacagctatgaattac-taaaaaaatgtt-
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TTTGGACCTTGATGTTCTTTTCTATCCTTGTCCAAGAAATGGCCCAAATTTCCGTCAAAAGGTTCTAGAGATGGGTGGCAAACTGCAGTTCCCCTACATGgtaag--attgat--tccttaaatcaaacaacaaaacaaacttagttttttgttatgatttctggtgta-ttttaaaaagatgggactaaagttgactaatctaa
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S161_69V6.1 (Physcomitrella patens), 5'ss of exon 5
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctcca--taatttcttcagtttcttaggt-catatactcaattacttctgttctactt--ttacacagctatgaattactaaaaaaatgtt
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CTTGGACATCGATGTGATCTTCTACCCATGTCCGAAGAATGGTCCTAACTTCCGTCCAAAGGCTAATGAGATGGGCGGAAAGAAGCAATTTCCTTACATGgtctgaatcgaaacctgaagttacctactgttgctatgtagatgtttaaacgtgaat-ctccagtaagaattagtttgtctgcgttcatttttcgtcggag----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|58590549|gb|CF988857.1|CF988857EST: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATG GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
genomic: TCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagt ... tatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTGGACCTTGATGTTTTGTTTTACCCCTGCCCTAAAAATGGCCCCACTTTCCGTCCAAAGGTTTTAGAGATGGGCGGAAAGCAACAATTTCCTTACATGgtatgcaagtaatcctccataatttcttcagtttcttaggtcatatactcaattacttctgttctacttttacacagctatgaattactaaaaaaatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA