Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgggtcgaattaccttcagagatactatctgaatcttgatggtgctcgcccaataacaaaattgcgcttctccccagGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGCTCCCGCTGCTTTTGAGGAATGTTGAACGCAACAAATCTTGGATTTCACA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g57330.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g57330.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013981_T02 (Zea mays), 3'ss of exon 3
gtaagatgggtcgaattacct-tcagagatactatctgaatcttgatggtgct--cgcccaataacaaaattgc--gcttctcccc-agGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGCTCCCGCTGCTTTTGAGGAATGTTGAACGCAACAAATCTTGGATTTCACA
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gtaggttgaattcaactatccatccaatgtatt-tctggatcctagtcctatcggcgttcacttttaaaattgtttgcttctcctttagGAATGGCCTTGTTGGGTGGTGATGTTACAACAACTGACCAAGCCGAGGTGCTCCCACTGCTTATGAGAAATGTTGAACGGAACAGATCTTGGATCTCACA
upper sequence: LOC_Os02g57330.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G471805_T01 (Zea mays), 3'ss of exon 4
gtaagatgggtcgaattacct-tcagagatactatctgaatcttgatggtgctcgc--ccaataacaaaattgc--gcttctcccc---agGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGCTCCCGCTGCTTTTGAGGAATGTTGAACGCAACAAATCTTGGATTTCACA
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gtaagctcaatttaactgcccgtcagatgtatt-tcaggatcttagtcctattggcttcctcttttaaaattgtttgcttatctcctttagGAATGACCTTGTTGGGTTGTGATGTTACAACAACTGACCAAGTCGAGGTGCTTCCGCTGCTTATGAGAAATGTTGAACGCAACAGATCTTGGATTTCGCAMapped 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|27576395|gb|CA999089.1|CA999089EST: AGGAAAAAGGGTGATTGAGCTAGGAGCTGGTTGTGGTCTAGCTGGGCTTG GAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGC
genomic: AGGAAAAAGGGTGATTGAGCTAGGAGCTGGTTGTGGTCTAGCTGGGCTTGgtaagatggg ... ttctccccagGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactatctgaatcttgatggtgctcgcccaataacaaaattgcgcttctccccagGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGCTCCCGCTGCTTTTGAGGAATGTTGAACGCAACAAATCTTGGATTTCACA
caataac putative branch site (score: 2)
ttgcgcttctcccc putative PPT
aataacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgggtcgaattaccttcagagatactatctgaatcttgatggtgctcgcccaataacaaaattgcgcttctccccagGAATGGCTTTGCTGGGTTGTGACGTGGTTACAACAGACCAAGTTGAGGTGCTCCCGCTGCTTTTGAGGAATGTTGAACGCAACAAATCTTGGATTTCACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT