Sequence
atgc intronic sequence ATGC exonic sequence...tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095670_T02 (Zea mays), 3'ss of exon 1
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgc--attgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA-----------------------
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---------------cattgcaattacatcatatgtattgaagattatgtctacattaatattatgttggccctttttcttacttc-attacatgttcccaggacattcattggagT----GCTCC-----ATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAATCCGTGAGTTGGATG
upper sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 1
tagtgtccatt-atgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA--------------------------
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---aatccatttgcaatcacattagatttaatgatttattgaagattatgtttacataagtattatgt----tggctcttttgcttactccat---------------ttaca-----taatgccagGACATTTATTGAGACATCATGCCTAAGATAAAGACAAGTCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACCATCCGTGAGTTGGATGCCA
upper sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095670_T01 (Zea mays), 3'ss of exon 1
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgc--attgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------
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-tgcttttattaatgcattgcaattacatcatatgtattgaagattatgtctacattaatattatgttggccctttttcttacttc-attacatgttcccagGACATTCATTGGAGT----GCTCC-----ATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
upper sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 1
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------
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-tgcttttattaatgcattgcaattacatcagatgtattgaagattatgtttacataaatattatgt----tggccctttttcttacttcat----taaatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
upper sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020728_T02 (Zea mays), 3'ss of exon 1
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA-----------------------
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---------------cattgcaattacatcagatgtattgaagattatgtttacataaatattatgt----tggccctttttcttacttcat----taaatgttcccaggacattcattggagTGCTCCATTCATTGAGACAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAATCCGTGAGTTGGATGMapped 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|33794327|gb|CF323050.1|CF323050EST: CGCGCGCCACAGCTTCCATTCGGCGACTGCAAGGGCGCCCAAGCCAAGAG GGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTA
genomic: CGCGCGCCACAGCTTCCATCCGGCGACTGCAAGGCCGCCCAAGCCAAGAGgttattattc ... atgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTA
EST:
gi|29686606|gb|CB682881.1|CB682881EST: CGCGCGCCACAGCTTCCATCCGGCGACTGCAAGGCCGCCCAAGCCAAGAG GGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTA
genomic: CGCGCGCCACAGCTTCCATCCGGCGACTGCAAGGCCGCCCAAGCCAAGAGgttattattc ... atgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA
atcttac putative branch site (score: 3)
tgtcctc putative PPT
taaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT