Sequence
atgc intronic sequence ATGC exonic sequenceGGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctgtacttctatcatagcctttatgtttgtgttgtgattgtaatagagtaactgccaaattgtaagatcagctttaattttggctgctatttttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g08980.3 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G104133_T01 (Zea mays), 5'ss of exon 4
GGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctgtac--ttctatcatagcctttatgtttgtgttgtgatt-gtaatagagt-aactgccaaattgtaagatcagctttaattttggctgctatttttt
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GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTAGGAGCACTGGGTTACGGTTATATGTGGTGGAAGgtatgtttctcccttttatcgctgcttctatgtattcttggttgttcgtaatttctttgacattttaactgctga--cattgtaggatctgtctgctttctc--
upper sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G558539_T01 (Zea mays), 5'ss of exon 5
GGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctgtac--ttctatcatagcctttatgtttgtgttgtgatt-gtaatagagt-aactgccaaattgtaagatcagctttaattttggctgctatttttt
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GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAAgtatgtttctcccttttgtcacagcttctatgttttcttggttgttagcaattgttttgacattttaactgctgaaattg--taggatatgtctgctttctt--
upper sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G04980.2 (Glycine max), 5'ss of exon 5
---GGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatg---ctgtacttctatcatagcctttatgtttgtgtt--gtgattgtaatagagtaactgccaaattgtaagatcagctttaattttggctgctatttttt
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GTAATTTATCATCCCTTGTCGTTCCAGCTGCTGCCTTGGGCGCTCTGGGTTATGGCTACATGTGGTGGAAGgtatggaactgcttgcctacttggattcttgtgcattctttcaatagtttcattggtttatggttgaaattgtattgt-atttttcttttttaccagtatg----
upper sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0026g01700.t01 (Vitis vinifera), 5'ss of exon 5
---GGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctg-tacttctatcatagcctttat-gtttgtgttgtgattgtaatagagtaactgccaaattgtaagatcagctttaattttggctgctatttttt------
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GCAACATAACATCACTTGCAATCCCAGCTGCCACCTTGGGGGCATTGGGATATGGTTACATGTGGTGGAAGgtatgataataagttgtggatatttttcctcgtttctcttttgcttg-----gggaaagtgt---agtgaaggggcacccctgttacaggttgtcagttattaaaaatMapped 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|218505037|gb|FG952955.1|FG952955EST: TACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAG GGCATCTCCTTTGCGGACCTAATGTATGTGACTAAGCGTAACATGGCAAAT
genomic: TACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctgta ... tgttatccagGGCATCTCCTTTGCGGACCTAATGTATGTGACTAAGCGTAACATGGCAAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAGgtatgctgtacttctatcatagcctttatgtttgtgttgtgattgtaatagagtaactgccaaattgtaagatcagctttaattttggctgctatttttt
- - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG