Sequence
atgc intronic sequence ATGC exonic sequenceTGCTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAAgtgagctcttgttatccatgtttacgtgcttacatttgtatcagttgtttctgctacaaaccatcatttgaaaagaaacttactgggttttgcttaaccag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g41120.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G044457_T01 (Zea mays), 5'ss of exon 9
TGCTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAAgtgagctcttgttatccatgtttacgtgcttacatttgtatcagttgtttctgctacaaaccatcatttgaaaagaaacttactgggttttgcttaaccag
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TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAAgtgcagtctt----------tcttcgtacatgaat--gtttcagtt-------ctatggtttaacgctgcataaagaacttaccgagtttt--ctgtccag
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G161019_T04 (Zea mays), 5'ss of exon 10
TGCTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAAgtgag-ctcttgttatccatgtttacgtgcttacatttgtatcagttgtttctgctacaaaccatcatttgaaaagaaacttactgggttttgcttaaccag
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TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAAgtgagtctttcatcatgcatgtatg-----ttgcagttgtatggcttaatggtgc----------------ataaaaaacttaccgagttt--cctattaagMapped 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|29642620|gb|CB647627.1|CB647627EST: CTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAA GTTGTTCCTACAATTTACACTGATCTAAGAGGGCGCAAGATTCATTCCAAC
genomic: CTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAAgtgagctctt ... gcttaaccagGTTGTTCCTACAATTTACACTGATCTAAGAGGGCGCAAGATTCATTCCAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTCAGTGGACACAACCAGCATCAGATGGGACATACCAATACTTCATAAAAgtgagctcttgttatccatgtttacgtgcttacatttgtatcagttgtttctgctacaaaccatcatttgaaaagaaacttactgggttttgcttaaccag
- - AGTGGA
- - - - - - - - - - - CAGATG