Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgattttctctaaattttggagtgcaatactgcaagaaatagtcacattaatatttttttgaaattcttttcgagttggagtcggttggtttgccctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g03920.5 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g03920.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 7
gtaagtgattttctctaaattttggagtgcaatactgcaagaaatagtcacattaa-tatttttttgaaattcttttcgagttggag--tcggttggtttgccctcattaa----gCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC------------------
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gttagt-acatagtctgttctgttga-tgcagaaattaatcctgcatttccactgagtatgatctcatgaagcttttctctttagatgtttttttgaagttttctcatcaacaaagtaatgtcaaaatttgcagCACCGCCAGAAGAACTGTACGCCACACAATTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAAGAGAACATCCGAGCCTTGGCCGCTACCGCTGG
upper sequence: LOC_Os03g03920.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G057158_T01 (Zea mays), 3'ss of exon 7
gtaagtgattttctctaaattttgg-agtgcaatactgcaagaaatagtcacattaa---tatttttttgaaa---ttcttttcgagttggagtcggttggtttgccctcattaa----gCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC------------------
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gttagtagtacatagtctgttctgttaatgaaaaaaataatcctgcatttccactaagtataatctcttgaagcttttctctttggatgttttttttttgaggttttctcatcaacaaagtaatgtcaaaatttgcagTGCCACCAGAAGAACTGTATGCAACACAATTAGCTCAGCTCCAAGAAATGGGTTTTTTTGACACACAGGAGAACATCCGAGCCTTGGCCGCCACTGCTGG
upper sequence: LOC_Os03g03920.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G22530.1 (Glycine max), 3'ss of exon 8
gtaagtgattttctctaaattttggagtgcaatactgcaagaaatagtcacattaatatttttttgaaattcttttcgagttggagtcggttggtttgccctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC------------------
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----------------gaatggacaaaaaatgccccccaaaacatagggacctaggtattattt--acctaaattttatactctgctcagc-------ctctcactga-ctttgttg-tcttgtcagAGCCGCCAGAGCAGCTGTATGCCTCCCAACTTTCACAGCTTCAAGAGATGGGATTCTTTGACACACAAGAGAACATTAGAGCTCTTATCGCCACTTCAGG
upper sequence: LOC_Os03g03920.5 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0210g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtgattttctctaaattttggagtgcaatactgcaagaaatagtcacattaatatttttttgaaattcttttcgagttggagtcggttggtttgccctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC------------------
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----------------------------------------gttattgctctctttctctctctcacatgtgtttatttact--aattattctgattctcaacctgtgttccattttgttcttc-cagTACCACCGGAACAATTGTATGCTACTCAGCTGTCGCAGCTTCAAGAAATGGGTTTCTTTGACACACAGGAGAATATACGGGCTCTGACTGCCACTGCAGGMapped 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|86426364|gb|CI071461.1|CI071461EST: CAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG CAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAG
genomic: CAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATGgtaagtgatt ... cctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatttttttgaaattcttttcgagttggagtcggttggtttgccctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC
cattaat putative branch site (score: 3)
tttgccctc putative PPT
ttttttgaaattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgattttctctaaattttggagtgcaatactgcaagaaatagtcacattaatatttttttgaaattcttttcgagttggagtcggttggtttgccctcattaagCAATGCCAATATTTGCAGTTCCACCAGAAGAGCTATATGCAACACAACTAGCTCAGCTCCAAGAAATGGGTTTCTTTGACACACAGGAGAACATTCGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA