Sequence
atgc intronic sequence ATGC exonic sequencegtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g13770.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagc-gattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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---------------------------------------------------gtacgtttgtttctctgcacatttgcttcatcacctgttc-----tgtcctgtgtaaacatgggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 2
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatctt-----gtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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---------------------------tgtgttgtgtccatgaagaacagaaagactttattacgtgtggctgtgatcgccccga-gtgttgaaattaccattttgtccttattcttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTCAACAAGAAGATCTACAATTACTTCCCCTATCCATA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtatggttttctgccacaataatcgcgtgacctacacctctgcgtt-----gtttattgaattgaattgatttc--acagcgattattcagctgtttgaagattgccattttgtgcaagtgatctt-----gtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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gtacgtcacgtgactctgttcttattacacgcaaaaaacaacctatgattgtgtcgtgtgctcctgttctgtgtctcttacgttccctaagcttaaacttttaaccacttaacagatagacttcatgtgtggctgtgatcgttccga-gtgttgaaattacggttttgtccttttccttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCCTATCCATA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttg---tgcaagtgat-cttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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gtacgtatcattcacgcgcttttcttaaaacgt-tatc-ctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 2
gtatggttttctgccacaataatcg-cgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcag-----ctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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gta-ggtcatcaccgttaccaactaacaacatctacaattct-cttcaacggtcagaaagagtcaaaataa-aatggtgattcaaaatccctgtttctgggt-gtctttaccaaattgtactttttcagGTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------gtatggttt--tctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctg-aaaactgcgtc-ttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaaaatgtaatgcttgttgtgtattagGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA
upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgt---agGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
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--------------------ggctgcgctgtttgaa--tatgcatcatgagatgcattcccttcttttt---gtggttgtctaga-gtttcagggctatgatgccgtgatgcctgttgtgtgtcagGTACTTCCTGAATGTTATCTTCAACATCATGAACAAGAAGATCTACAACTACTTTCCCTACCCTTAMapped 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|29661884|gb|CB658159.1|CB658159EST: TTCCTGGAGAAGTACCCTGCCTTGATCACCGGCTTCTTCTTCTTCATGTG GTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTA
genomic: TTCCTGGAGAAGTACCCTGCCTTGATCACCGGCTTCTTCTTCTTCATGTGgtatggtttt ... gatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTA
EST:
gi|25797136|gb|CA753097.1|CA753097EST: CCGGCTTCTTCTTCTTCATGTG GTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTA
genomic: CCGGCTTCTTCTTCTTCATGTGgtatggtttt ... gatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
attattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttgtgcaagtgatcttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG