Sequence
atgc intronic sequence ATGC exonic sequencegtgatttttcatttttcttatcaattggttaggctattttatcataacttgttcatgtcttataacatcagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g45350.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G020574_T04 (Zea mays), 3'ss of exon 6
gtgatttttcatttttcttatcaattggttaggctattttatcataacttgttcatgtcttataacat-cagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT
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--------gtgatttccttacatattgat-atgttgtattattagtaattgtcatttttaaaatttatgttgtcttatttttttcagGGAGCAAAGGTACATCAGACGCAGAGCCTAACAGTAAAAAAGATCAATTAGTGTTGGACATATGTGTCATATGCCTTGAGCAAGAGTACAATGCTGTTTT
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 9
gtgatttttcatttttcttatcaattggttaggctattttatcataacttgttcatgtcttataac-atca-gttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT
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--------gtgatttccttatatattgat-atgttgtattattaatgatcgt-cgtgtttaattattatcttgtattattttgttcagGGAGCATTGGTTCATCGGACACAGAGCCTAACAGTAAAAAAGACCAATTAGTGTTGGACATATGTGTCATATGCCTTGAGCAAGAGTACAATGCTGTTTT
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 9
gtgatttttcatttttcttatcaattggttaggct-attttatcataacttgttcatgtcttataacatcagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT---
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--------gtaaattgtttatggctcaattatatttgtttttgcaatgcctgtttcaatagt-taccaaaatttgtggttctttctcagTTGAAAAGGCCGACAGCT-TATCAGATGGTGCTAAAAAGGATCGCTTAATGCCAGATTTGTGTGTAATATGCCTTGAGCAGGAATATAATGCTGTTTTTGT
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 9
gtgatttttcatttttcttatcaattggttaggct-attttatcataacttgttcatgtcttataacatcagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT---
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--------gtaaattgtttatggctcaattatatttatgtttgcaatgcctgtttcaatagt-taccataatttgtgattctttctcagTTGAAAAGGCTGACGGCT-TATCAGATGGTGTTAAAAAGGATCGCTTAATGCCAGATTTGTGTGTAATATGCCTTGAGCAGGAATATAATGCTGTTTTTGTMapped 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|33683627|gb|CF311866.1|CF311866EST: GGTTCATGCTGCTGCTGCACAAAGACAAGCTAGAGAAGCTGAAG GGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGG
genomic: GGTTCATGCTGCTGCTGCACAAAGACAAGCTAGAGAAGCTGAAGgtgatttttc ... ttttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGG
EST:
gi|86905521|gb|CI285484.1|CI285484EST: GGTTCATGCTGCTGCTGCACAAAGACAAGCTAGAGAAGCTGAAG GGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGG
genomic: GGTTCATGCTGCTGCTGCACAAAGACAAGCTAGAGAAGCTGAAGgtgatttttc ... ttttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctattttatcataacttgttcatgtcttataacatcagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT
ttataac putative branch site (score: 2)
ttttatttt putative PPT
ttataacatcagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttttcatttttcttatcaattggttaggctattttatcataacttgttcatgtcttataacatcagttttattttgtacagGGGGCAATGGTACATCAGATGTAGATTCTAACAATAAAAAGGATCAATTGGTCTTGGACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT