Sequence
atgc intronic sequence ATGC exonic sequenceGGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataaattgagagatatgcaacccctagaggttcttccacagctgctaatataattaacagaagtctaccatagc...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g46060.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G123387_T01 (Zea mays), 5'ss of exon 3
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataaattgagagatatgcaacccctagaggttcttccacagctgctaatataat-taacagaagtctaccatagc------
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GGTTCTGCTTCCAGACAAGGAGCGACGTGGATGTGCTGGACGACGGCTACAAGTGGAGAAAGTACGGCCAGAAGGTTGTCAAGAACAGCCTCCATCCAAGgtatgcgcgcgca------gcgatctatatattcggcgat-cctaaccctaatgcctcgtttcgaacatgatttccccccactgcaggctgctgctatgggaatcga
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G25770.1 (Glycine max), 5'ss of exon 3
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataa--attgagagatatgcaacccctagaggttcttccacagctgctaatataattaacagaagtctaccatagc
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GGTTTTGTTTCCAAACAAGAAGTGATGTAGATGTGCTTGATGATGGTTATAAATGGAGGAAGTATGGTCAGAAAGTTGTCAAGAATAGCCTTCACCCAAGgta-atatatatataatccttgaaccttaattaccccttgctttcttaattatatagttttgctcagttttgcaagt-tctttgaataaatttgaagatcat
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G37930.1 (Glycine max), 5'ss of exon 3
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataaattgagagatatgcaacccc-tagaggttcttccacagctgctaatataattaacagaagt--ctaccatagc
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GGTTTTGTTTCCAAACAAGAAGTGATGTAGATGTGCTTGATGATGGTTACAAATGGAGGAAATATGGCCAGAAAGTTGTCAAGAATAGCCTTCATCCAAGgta-atattcaaatcttgattaac-catgactttt-atttgctcattatagtaaacatatgttttaaggaaaaataataatgagttgaattaattaacacatg
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G44745.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataaattgagagatatgcaacccctagaggttcttccacagctgctaata--taattaacagaagtctaccatagc---
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GATTCTGTTTCCAAACCAAAAGCGATGTTGATGTTCTTGACGATGGCTACAAATGGCGTAAATATGGTCAGAAAGTCGTCAAGAACAGCCTTCACCCCAGgtac-taaattagttaattatcat-caccacc--acatatatgtgactgcttaggcttcattaact-ttaccaatagtttcctaatataacatgtccttaattag
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv15s0021g01310.t01 (Vitis vinifera), 5'ss of exon 3
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatata--cacgaaacataat-acataaattgagagatatgcaacccctagaggttcttccacagctgctaatataattaacagaagtctaccatagc
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GGTTCTGTTTTCAAACTAGAAGCGAGGTGGATGTGCTCGACGATGGTTACAAATGGAGAAAATATGGCCAGAAAGTCGTCAAGAATAGCCTTCATCCAAGgtaacattactgcctccaaaaataattaaattgcctcataaattttcttatactaacatcatacatagggcatagaatttcccctctggaggtggacaat---
upper sequence: LOC_Os04g46060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S235_126V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTTCTGCT-TCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtat---atatatacacgaaacataatacataaattgagagatatgca--acccctagaggttctt----ccacagctgctaatataattaacagaagtctaccatagc
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-GCTACGCGATTAAAACCAGGACTGATACTGATGTAATGGATGATGGTTACAAGTGGAGGAAGTATGGACAGAAGGCTGTCAAAAAAAGCCCTCACCCCAGgtactgaactttttcaagaaa-atctcaggaaacgtggtaggtttttcttgtcgttagtgtctccttgcgctacaactgcctgcagtcaaatcaggaactc--------Mapped 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|88902167|gb|CI374775.1|CI374775EST: AAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAG GAGCTACTACAGGTGCACCCACAACAACTGCCGCGTGAAGAAGCGGGTGGA
genomic: AAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatat ... gcaaatgcagGAGCTACTACAGGTGCACCCACAACAACTGCCGCGTGAAGAAGCGGGTGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGTTCTGCTTCCAGACCAGGAGCGATGTGGATGTGCTGGACGACGGCTACAAGTGGAGGAAGTATGGCCAGAAGGTTGTCAAGAACAGCCTCCACCCAAGgtatatatatacacgaaacataatacataaattgagagatatgcaacccctagaggttcttccacagctgctaatataattaacagaagtctaccatagc
- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacccc