Sequence
atgc intronic sequence ATGC exonic sequencegtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g44922.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 8
gtattttttttgtgcgatgtgtctatttt-tgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtaatattct-gcaagatatgtttactttctattcaaaagccgtctctacataccccattaatatggccactcatgtgaa--tgtgacacacaaatc------------tattgatt-ttagATCATCGACAAGTCTTTTGGTTTTGATACGGCTGTGGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
----gtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgagattatgactta-ttgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtgagcatgcttgaattg-gacatctgaagccttacaatagaagctactttgctgaaaatataaaaaggat--ttacttttaaactgtcacctaattaaccatgttg-----tacctgaatc--agGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
gtatttttttt----gtgcgatgtgtctatttttgtgtagaaat------ttgttgtacgcatgctgttcagttgacggttca-tacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatctgaagtgttagttctctatgaggaaacttcatcatgttcggattgtcttcttttt---ctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
gtatttttttt----gtgcgatgtgtct-atttttgtgtagaaat------ttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggtt-atctatgaaga-aacttcatgttcggattgccttcttttt---ctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
gtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgag-attatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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--gtacttcttgcctattgcacctgaattaattttg----ttcttttctccatctttttcaataaaccttgcattagcctgtaatgtgtcttcaccttagactgccttctcttgattc--agGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------gtattttttttgtgcg---atgtgtctatttttgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttat---tgcttatgttacctttttcttgat-tcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgttttcttga-agtccaagtgtgccaccgtctaatgcatatttgtcgaatgtggtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
----------------gtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtac-gcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
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gtacgttttagacacggaaattcaacaacacgatggaat--tctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaa----atatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTGMapped 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|569752|gb|D40601.1|D40601EST: TAAAGGTTTCTGTTGCTGGGATTCCCAAGACAATAGATAATGACATAGCG ATCATTGACAAGTCATTTGGTTTTGATACGGCCNTAGAAGNGGCCCAGCGT
genomic: TAAAGGTTTCTGTTGCTGGGATTCCCAAGACAATAGATAATGACATAGCGgtattttttt ... tgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGT
EST:
gi|27576264|gb|CA998958.1|CA998958EST: CCCAAGACAATAGATAATGACATAGCG ATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGT
genomic: CCCAAGACAATAGATAATGACATAGCGgtattttttt ... tgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGT
EST:
gi|571842|gb|D41353.1|D41353EST: TAAAGGTTTCTGTTGCTGGGATTCCCAAGACAATAGATAATGACATAGCG ATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAAGAGGCC-AGCG
genomic: TAAAGGTTTCTGTTGCTGGGATTCCCAAGACAATAGATAATGACATAGCGgtattttttt ... tgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAA-GAGGCCCAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
tcttgat putative branch site (score: 4)
cctttttcttgattct CT-rich tract
ttatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtacgcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG