Sequence
atgc intronic sequence ATGC exonic sequence...gtgaaaacttgcatctgttttaatattgtactgctactttatattttctccttacagtttcagatgggattaagttaattaacttttttctatgtatcagGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g40570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G372877_T01 (Zea mays), 3'ss of exon 2
gtgaaaacttgcatctgttttaatattgtactgctactttatattttctccttacagtttcagatgg--gattaagttaattaacttttttctatgtatcagGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT
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gtaattaacaaggcccttctttgttcttta-tgaaatcgtccaactttaattggctgatgaatatagctagctgtttgtattgacttggttccctgtatcagGCAGTGATCATGGGGTCAAAGCTCACGGGGACGGTTGGCTGTTGACCGTAGCGCTTATAGAAGGCACTGGCATCATAGCTACTGGCTCATCTGACCTCTT
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaaaacttgcatctgttttaatattgtactg-ctactttatattttctccttacagtttcagatgg-------gattaagttaattaacttttttctatgtatca------------gGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT-
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-------gtaacatccatgaagatacagcatcgaccatttcatattctttc-ttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCT-AGCAGCTGTAGATCCAAGCGGGCATTGMapped 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|58681959|gb|CK070646.1|CK070646EST: GCTTCTTAAATGCATGGAAACAAAAAG GTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTG
genomic: GCTTCTTAAATGCATGGAAACAAAAAGgtaccttatc ... tatgtatcagGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctccttacagtttcagatgggattaagttaattaacttttttctatgtatcagGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT
aattaac putative branch site (score: 2)
cttttttctat CT-rich tract
attaagttaattaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaaacttgcatctgttttaatattgtactgctactttatattttctccttacagtttcagatgggattaagttaattaacttttttctatgtatcagGTAGTGATCATGGGGTCAAAGCTCATGGTGATGGTTGGTTGATGACTGTTGCACTTATTGAGGGCACTGGTATCACTAATTCTAATTCAAAAGAATTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - acttgca
- - - - - - -tctgttt
- - - - - - - - - - - - - - - -tgctact