Sequence
atgc intronic sequence ATGC exonic sequence...aattattttgtattattttcactttatttatgcttttttggggttgaatgctaaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59350.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G019907_T02 (Zea mays), 3'ss of exon 1
aattattttgtattattttcactt-tatttat--gcttttttggggttgaatgct---aaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
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----gtttggaaccatcacaatttctataaaccagtttcttaaaaaccggatgcttccaaacagggcctaaagtatcccagtttactaattatatg--cctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCTTCTGATTCTAGTGACAAATCAAGGGACAAACTAGATCAGAAG
upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 5
------aattattttgtattattttcactttatttatgcttttttggggttgaatgctaaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
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tatgcttatctttttgtaacatttatgttgtgcttatctttttgtaacattta----tcagcatatactaaagtataccagtttactaattatctg--cctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAATCAAGGGACAAACTAGATCAGAAGMapped 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|33793551|gb|CF322658.1|CF322658EST: CAAGGACTGATACATCAACAGATCCAGACACTGATGAGAGGAATCAGATG TTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGG
genomic: CAAGGACTGATACATCAACAGATCCAGACACTGATGAGAGGAATCAGATGgtaataagac ... tacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgctaaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
tgctaaa putative branch site (score: 2)
taaatttatactcaat 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
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aattattttgtattattttcactttatttatgcttttttggggttgaatgctaaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA