Sequence
atgc intronic sequence ATGC exonic sequence...gtagaaacattactttatctgctttcattgatgttctctattcttttggagcatatgttttatattagctgaagttactcaagtttcctttcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTTATTATGGGCCAAAAACATCTTCTGAAGACCATTAAGAGGAGGAAGAAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g12370.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g12370.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G026742_T01 (Zea mays), 3'ss of exon 1
gtagaaacattactttatctgctttcattgatgttctctattcttttggagcat--atgttttatattagctgaagttactcaagtttcctttcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTTATTATGGGCCAAAAACATCTTCTGAAGACCATTAAGAGGAGGAAGAAGT
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--ctagctattattttgtccgcatgtttctgtgctgtaagttcatgttgaatgttaacttctattgtttcatgaattcactagtgttcttcttcataattagGGATTTCATAAAGTTGATCCAGATAGATGGGAATGGGCCAATGAAGGTTTTATTAAGGGCCAAAAACATCTTCTGAAGACCATCAAGAGAAAGAAGAAAT
upper sequence: LOC_Os03g12370.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118485_T02 (Zea mays), 3'ss of exon 2
gtagaaacattactttatctgctttcattgatgttctctattctt-ttggagcatatgttttat-attagctgaagttactcaagtttcctttcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTTATTATGGGCCAAAAACATCTTCTGAAGACCATTAAGAGGAGGAAGAAGT
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-actaactattattttgtccacatgt-tctatgctgtatgctcatgttgaatcttaacctctgtcgtttcatgaattcactagtgttctttttcattatcagGGATTTCATAAAGTTGATCCAGATAGATGGGAATGGGCCAATGAAGGCTTTGTTAAGGGCCAAAAACATCTTTTGAAGACCATCAAGAGAAAGAAGAAATMapped 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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggagcatatgttttatattagctgaagttactcaagtttcctttcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTTATTATGGGCCAAAAACATCTTCTGAAGACCATTAAGAGGAGGAAGAAGT
tttcctttcat CT-rich tract
atatgttttatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaaacattactttatctgctttcattgatgttctctattcttttggagcatatgttttatattagctgaagttactcaagtttcctttcataatcagGGATTTCGTAAAGTTCACCCTGATAGATGGGAGTGGGCCAATGAAGGTTTTATTATGGGCCAAAAACATCTTCTGAAGACCATTAAGAGGAGGAAGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT