Sequence
atgc intronic sequence ATGC exonic sequence...tttgatcgctaaaattttcttgttgattaattgtaattagggtggtcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g45840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G170148_T01 (Zea mays), 3'ss of exon 1
-tttgatcgctaaaattttcttgttgattaattgta--attagggtggtc--aatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
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ctgtgattgtttataatttgtaaattgtaaatggtgctaccgtgataacttggatgatttaatgaaatttctcaaat-----tgatttttttttatttcttgtagTTTTGATCGTGATTGGAAGAAGATTGAAGCATATGTCGGCTCGAAGACTGTTATACAG
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 1
------tttgatcgctaaaattttcttgttgat-taattgtaattagggtggtcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
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attgtttatagtttgtaaattgtaagtgatgctactatgagaacttggttcattta-atgatatttatatttctcaaat------tttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 1
-tttgatcgctaaaatt--ttcttgttgattaattgtaattagggtggtcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
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gtttcaa-attaaagctagtgtttgtttctcccctttctttatcttggg-gtcgccatttgccactatcctcactttttttccccttcatttctgtt-ttcagGTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAGMapped 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|33678202|gb|CF306441.1|CF306441EST: GAGAGCTGGACGGAGCCCGAGCACGACAAGTTCCTCGAGGCGCTGCAGCT GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGT
genomic: GAGAGCTGGACGGAGCCCGAGCACGACAAGTTCCTCGAGGCGCTGCAGCTgtgagtgccc ... tttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
gtttgat putative branch site (score: 5)
cttccttttcttttgt CT-rich tract
ttttgtttgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgatcgctaaaattttcttgttgattaattgtaattagggtggtcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC