Sequence
atgc intronic sequence ATGC exonic sequence...tgtactatattaataacatttttattgttcatttggtgggtgtttcctgtaattagctaattattccatcaccttgaccatattttatgttgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g12810.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g12810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G413069_T01 (Zea mays), 3'ss of exon 10
----tgtactatattaataacatttttattgttcatttggtgggtgtttcctgtaattagctaattattccatcaccttgaccatattttatgttgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
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caagaatactgccttc-tgttctttttctcgttc-tgcattgcatttttctataaatatacctattatcacatctttacgaa-acatttcttgttgc-ttgcagCCAGAGTGGATGGCACCTGAGGTACTACGAAATGAACCATCTAATGAGAA
upper sequence: LOC_Os02g12810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g01310.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------------tgtactatattaataacatttttattgttcatttggtgggtgtttcctgtaattagctaatt-attccatcacct-tgaccatattttatg-ttgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
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gtaatactcttaaaacattaggacgattctatgctcttgcttttgcaaacttttcatttcatcatttcatcccaataagata--agaggcacagtgtgttcttttatcaaaatatgagatcattgattgtatcagtaataataaagttttgcggttgaactgcagCCTGAGTGGATGGCACCAGAAGTTCTAAGGAATGAGCCATCGAATGAAAAMapped 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|33692624|gb|CF320863.1|CF320863EST: TTCCTGTCCTCTAAATCAACAGCTGGAACAGTAATATCCTTGATGCTCTG CCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
genomic: TTCCTGTCCTCTAAATCAACAGCTGGAACAGTAATATCCTTGATGCTCTGgtgactttct ... tgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtaattagctaattattccatcaccttgaccatattttatgttgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
aattagctaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtactatattaataacatttttattgttcatttggtgggtgtttcctgtaattagctaattattccatcaccttgaccatattttatgttgggctacagCCGGAGTGGATGGCACCAGAGGTTCTACGTAATGAGCCATCAAATGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - -aataaca
- - - - - - - - - - - - - - tcatttg