Sequence
atgc intronic sequence ATGC exonic sequenceGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac...
Basic information
species | Oryza sativa |
transcript | LOC_Os11g29190.4 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156673_T02 (Zea mays), 5'ss of exon 1
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggta-accccccctttcgcgcttcgctcgcccaatctctttcgaacca-gtaaaattttaccgggatttgttagaac------------------------
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--------------------------AGGTCATGGCTGTCCGCATCATCAAGCATACCCTGGAGATCATCCACCTGCTCACCGATGCCAACCCCATCCAGGTCGTCGTCGACGCGATCATCAACAGgtacagtcttaatctcggctaataaccgttaaacctactcgttactatatgttgattccattcagtatgctggatccccccctgaaccgtgtgtgtattt
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 2
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac--------------------------
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--------------------------AGGTCATGGCCGTCCGCATCATGAAGCACACCCTGGAGATCATCCACCTGCTCACTGACGCCAATCCCATCCAGGTGGTCGTGGACGCCATTATCAACAGgtactaccttgctctcctgtcctcactcccgatctctgtattgtcaggctaataacagctaaacttgttactttatgctgatactttttggaatgcggta
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G26840.2 (Glycine max), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccag--taaaattttaccgg-----gatttgttagaac-------------------
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--------------------------AGCTCATGGCTGTCAGGATTATCAAGCATGCCATGGAGATCATCCACTTGCTCACTGACCTGAACCCAATTCAGGTCATTGTTGATGCCGTCATCAATAGgtatgttcgggtgttgagaacttcttttttttgtgttgatggatttgctttgggttttaattgcagatgagttgtttgtgctggtgtcatcaattgtaga
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G11940.2 (Arabidopsis thaliana), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatt--tgttagaac---------------
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--------------------------AATTGATGGCTGTCAGGATCGTCAAGCACGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgta--ctaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgtttgttgcttgagccag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggta-accccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac-----------------------
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--------------------------AGTTGATGGCTGTCAGGATCGTCAAGCATGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S101_208V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccct----ttc------------------gcgctt---cgctcgccca---atctctttcgaa-ccagtaaaattttaccgggatttgttagaac---------------------------------------------
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--------------------------AGTTGATGGCTGTACGCATCGTGAAGCACGCGATGGAGATTATTCACCTACTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac---------------------------------------------------------------------------------
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--------------------------AGTTGATGGCGGTGCGCATCGTGAAGCACGCGATGGAGATCATCCACCTGCTGACGGACCAGAACCCCATCCAGGTCATCGTGGATGCCATCATCAACAGgtaggttatc-tcgaacacttgtttagctgcatattggggggagaggcgggggatgggcgc-atgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggt---aaccccccctttc-----gcgcttcgctcgcccaat---------ctctttcgaa------ccagtaaaattttaccgggatttgttagaac-------------------------
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--------------------------AGTTGATGGCTGTCCGCATTGTGAAGCACGCTATGGAGATCATTCACCTTCTGACTGATCAGAACCCCATCCAGGTCATCGTTGATGCTATCATCAACAGgtttgaatcttatctttctattggtgtttgatgtggaaaatgaaatgcgacactcttgaggcgagtctaattcaattgtagcaatttttagtggcatgaggcatatcttttatctgctgcag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggt---aaccccccctttcgcgct-tcgctcgccca------atctctttcgaaccagtaaaattttaccgggatttgttagaac-------------------------
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--------------------------AGTTGATGGCTGTCCGCATTGTGAAGCACGCCATGGAGATTATCCATCTCCTGACTGACCAGAACCCCATTCAGGTCATCGTCGATGCTATTATCAACAGgttcggacgcaatcccgtgtgatatcgaacatcctgaggacacaattctttttctgattaaatattgtcaatttgtctctgagcgacagtgttttcccatacattgcag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac
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--------------------------AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgctt-gcag--------------
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac
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--------------------------AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag
upper sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37091 (Selaginella moellendorffii), 5'ss of exon 3
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac
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--------------------------AGTTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcagMapped 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|86423685|gb|CI062446.1|CI062446EST: AGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAG GGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGA
genomic: AGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcg ... ctggtgccagGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcgccc