Sequence
atgc intronic sequence ATGC exonic sequence...agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g51380.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 7
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttc-ttccttaatattatctatctaatataacaatttatt---atagAGT---TCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
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--cctaagcatttgttcttttattg--gtttggttgataccttttctataagcgtggaaggctcctgagtaatgataaaatgtgttggcgtgttccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGT---
upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 6
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA-----------------------------
||| || || || ||| || || || |||||||||||||| |||||||||||||| || ||||| |||||||| || |||||||| || |
------------------------------------------------------------------------------------------------------gcccggtgaagacaacttttgtatcgttttcgctgctatgggagTTAACATGGAGACAGCTACTTTCTTCAAACGTGATTTCGAAGAAAATGGATCTATGGAGAGAGTGACACTTTTTCTCAACTTG
upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
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----------------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagttt--ctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA
upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctat-ctaatataacaatttattat--agAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
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---------------------------------------gtacttttgttttccgtttatcttctgtctgttgttgagactgatgagtttctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGAMapped 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|66915737|gb|CX102585.1|CX102585EST: GTCAGGCTGGTCTGGTAAAGTGTTTAGAGAAGAGTGACAATATCTTGGAG AGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAAC
genomic: GTCAGGCTGGTCTGGTAAAGCGTTTAGAGAAGAGTGACAATATCTTGGAGgtatttttgt ... tttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
atataac putative branch site (score: 3)
ttccttaatattatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgcagttttctattctgttattgctgtatgctgaataacattttgacattcacacttcttccttaatattatctatctaatataacaatttattatagAGTTCCGAGGATGAAAATTTTGCGATTGTCTTTGCTGCTATGGGAGTAAACATGGAGACAGCACAATTTTTCAAGCGTGATTTTGAGGAAAATGGTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA