Sequence
atgc intronic sequence ATGC exonic sequencegtctaactccggctaaacataattgggttattgtcttgtttgtgttttaattctgatgtatatgagtgagttttctttaccatttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55410.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 4
-gtctaac-tccggctaaacataat-tgggttattgtcttgtttgtgttttaattctgatgta-tatgagtgagttttctttaccatt------tttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
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taaagaacatctgaacagacttgttgtgaggctttattatccttatcgttaaatggttatttgctaacagcaatgtatgtatatgattgcttacccttagCCTGGAGAGGAGCCATGCCCTCTGGACCCTTGGATTGCCGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 4
--------gtctaactccggctaaacataattggg-----ttattgt--cttgtttgtgttttaattctgatgtatatgagtgagttttctttaccatttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
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aataatcttgcatacaacagtaaagaacatttgaacagacttgttgttccttatcgttaaatggtttccaatagttatgtgtatgattg-tttatcatt----agCCTGGAGAAGAGCCATGCCCCCTGGATCCTTGGATTGCTGTCCCGGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAAAATCCTGAG
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 3
-----gtctaactccggctaaacataattgg-gttattgtcttgtttgt---gttttaattctgatgtatatgagtgagttttctttaccatttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
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gttcatctttaatgtgccttttgatatttgttgcaagtgctttatttgtaaagtcttgataatgatgcaagtgaatgggat----------tttattagCCGGGAGAAGAGCCATGCCCTATCGATCCTTGGATAGTGGTTCCTGATAAAAGCAAATATGTTGATCAACAGACCCTGAAATTGCAGGAGAATCCTGAGMapped 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|58671106|gb|CK059792.1|CK059792EST: CATGTTCCTCAG CCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAG
genomic: CATGTTCCTCAGgtctaactcc ... catttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttgtgttttaattctgatgtatatgagtgagttttctttaccatttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
ttctgat putative branch site (score: 3)
ttttctttaccatttt putative PPT
tgttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaactccggctaaacataattgggttattgtcttgtttgtgttttaattctgatgtatatgagtgagttttctttaccatttttcagCCTGGAGAAGAGCCTTGCCCCTTGGACCCCTGGATTGCAGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAGGAAAATCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG