Sequence
atgc intronic sequence ATGC exonic sequenceCAGCTTCGTGATCTGGGACTCGCACGCCTTCGAGCGCGACCTCCACAGGCACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgagattcccttgatccctgtgttcgtttgtttctgatgcgcgaattcggtgccatttccagttggttggacgaaatcggtagtgaaatctgagtttct...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g12370.3 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g12370.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G118485_T02 (Zea mays), 5'ss of exon 2
CAGCTTCGTGATCTGGGACTCGCACGCCTTCGAGCGCGACCT-CCACAG--GCACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgagattc-----ccttgatccctgtg---------ttcgtttgtttctgatgcgcgaattcggtgccatttccagttggttggacgaaatcggtagtgaaatctgagtttct
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---TTTCGTGATCTGGGACTCGCACGCTTTCGAGCGCGACCTGCTGCCGCGGCACTTCAAGCACAATCACTTCACCAGCTTCATACGCCAGCTCAACACCTACgtgagaattaccctccctgatcctcatgcctacattctctattagttccctgtgcgcgaaataaatgtggtttgc-gctgattaggcgcgattgttggttt-------------
upper sequence: LOC_Os03g12370.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G026742_T01 (Zea mays), 5'ss of exon 1
CAGCTTCGTGATCTGGGACTCGCACGCCTTCGAGCGCGACCTCCACA---GGCACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgag-attcccttgatccctgtg-ttcgtttgtttctgatgc-gcgaattcggtgc-catttccagttggttggacgaaatcggtagtgaaatctgagtttct
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---CTTCGTGATCTGGGACTCGCACGTTTTTGAGCGCGACCTGCTTCCGCGACACTTCAAGCACAACCACTTCACCAGCTTCATACGCCAGCTCAACACCTACgtgaggattacgcctagcctgatgctttattggatgaagctactgctaattgtttgcatgaaactttatgcttgtactgaa---atagtgacctatg-gtatca
upper sequence: LOC_Os03g12370.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EDP02415 (Chlamydomonas reinhardtii), 5'ss of exon 3
CAGCTTCGTGATCTGGGACTCGCACGCCTTCGAGCGCGAC---CTCCACAGGCACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgagattcc--cttgatccctgtgttc-gtttgtttctgatgcgcgaattcggtgccatttccagttggttggacgaaatcggtagtgaaatctgagtttct
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---CTTCATTGTATGGAAGCCACCGGAGTTTGCGCGGGACTTGCTACCCAAACACTTCAAGCACAACAATTTCTCCAGCTTTGTGCGCCAGCTCAACACCTATgtaagtccccggcaaggttgcagcaccaagcttgctacctaggttcaag--gaggggtgctgggaagagggggaatgcggctggggcggccgccggggagcc-Mapped 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|218490598|gb|FG960344.1|FG960344EST: ACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTAT GGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTT
genomic: ACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgagattcc ... tcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGCTTCGTGATCTGGGACTCGCACGCCTTCGAGCGCGACCTCCACAGGCACTTCAAGCACAGCAATTTCACCAGCTTCATACGCCAGCTCAACACCTATgtgagattcccttgatccctgtgttcgtttgtttctgatgcgcgaattcggtgccatttccagttggttggacgaaatcggtagtgaaatctgagtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA