Sequence
atgc intronic sequence ATGC exonic sequence...tttgtgctcggatttgtatcttaaagtctgatacttcttactgaaggggcctagatgatgttcggacaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAATGATGGGTCAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08544.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 2
tttgtgctcggatttgtatcttaaagtctgatact----tcttactgaaggggcctagatgatgttcgg-acaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAATGATGGGTCAGA
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tgtacacctgaactgaatttataagatcagctaatagaacagtactacagaaatc--accgtcgtcaggcaaaactgagtgaggct---aggattggttctgcagGGGCATCTCCTGGTGAAGGCACTGGAGCGACCATGTCTGATGATGAAGACAACCAGGTGGATAGCGAAGCCAACATGTTTGATGGAAATGATGGATCAGA
upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 3
tttgtgctcggatttgtatcttaaagtctgatacttct-tactg-aaggggcctagatgatgttcgg-acaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAATGATGGGTCAGA
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tgtacacctgaactgaaattgtgagagcagctaatagaacagtgcgatggaaatcgtcaatgtcagacaaaactgagtgattct---aggattggttctgcagGGGCATCTCCGGGTGAAGGCACTGGAGGAACCATGTCTGACGATGAAGATAACCAGGTGGATAGTGAAGCCAACATGTTCGATGGAAATGATGGATCAGA
upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 3
tttgtgctcggatttgtatcttaaagtc-tgatacttcttac---tgaaggggcctagatgatgttcggacaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAAT---GATGGGTCAGA
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----tgcacaaataaacagcaaaagcacacgactcgttttgcaattggaggagtactaaagtgatactagtattttttttatcacatggtgcatgatttaacagGAGTTTCACCCGGGGAAGGTACGGGAGCGACAATGTCTGATGAGGAAGATGAACAAGTAGATAGTGATGCCAATCTGTTTGATGGTGCTTTGGATGGTCC---
upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 2
--tttgtgctcggatttgtatcttaaagtctgatacttcttactgaaggggcctagatgatgttcggacaactgagttatgcttgtatgattggttctg--cagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAAT---GATGGGTCAGA
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atgatagtttctagtgtttgaagaaaatcttcaaactcttggttcaattagcc---acagcaagtaaacatataaat-gttctcacatgctgcatgataaacagGAGTTTCACCTGGAGAAGGTACAGGGGCAACAATGTCTGATGATGAAGATGACCAAGTAGATAGTGATGCCAATCTCTTTGATAGTAGTTTCGATGGGGC---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|2312070|gb|C28225.1|C28225EST: AGCAGTNATGGGGTGCTGGGAACTTGAACAGTCTTTACAAAGTCTAACAG GGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATA
genomic: AGCAGTGATGGGGTGCTGGGAACTTGAACAGTCTTTACAAAGTCTAACAGgtagaccaaa ... ggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATA
EST:
gi|88302049|gb|CI667895.1|CI667895EST: GGGGTGCTGGGAACTTGAACAGTCTTTACCAAGCTCTAACAG GGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGAT
genomic: GGGGTGCTGGGAACTTGAACAGTCTTTACAAAG-TCTAACAGgtagaccaaa ... ggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggggcctagatgatgttcggacaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAATGATGGGTCAGA
tatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtgctcggatttgtatcttaaagtctgatacttcttactgaaggggcctagatgatgttcggacaactgagttatgcttgtatgattggttctgcagGGGCATCTCCTGGTGAAGGGACTGGAGCGACTATGTCTGATGATGAAGATAACCAAGTGGACAGTGAAGCCAACATGTTTGATGGAAATGATGGGTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA