Sequence
atgc intronic sequence ATGC exonic sequence...taattcaattttcatgtggtccaatctcacctcgtcatgatatacacatggcgatggttgtcgggtgttgtatataatcatatatgtttgatatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g18360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g18360.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G853479_T01 (Zea mays), 3'ss of exon 1
-------------------------------taattcaattttcatgtggtccaatctcacctcgtca---tgatatacacatggcgatggttgtcgggtgttgtatataatcatata----tgtttgatatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA
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gtaagtatatatgcatcgtctagctagctaatacgttcattattaattaccacagatttgaattgtttgatttttaaacccaaggcaatggt-atcacatcttgcctgccatgtcataatattgtattgtatgattagTTGCTGATGCTATGGAGTACCATCAACGAGTTCCTCACGAGAAGCCTGCACATGTTCTCACCTATGAAGACCGGGATGGAGACTGGATGATGGTTGGGGA
upper sequence: LOC_Os01g18360.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074742_T01 (Zea mays), 3'ss of exon 2
----taattcaattttcatgtggtccaatctcacctcgtcatgatatacacatggcga-tggttgtcgggtgttgtatataatcatatatgtttgatatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA
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actctcagacacgtaaaaaagtgttgacaagtaaaaaaaaatgaaaggagtattgcaaatgcttgccggtcgctctata-----ataaatatgtgatatgattagATGCTGACGCTGTGGAGTACCATCAGCGGGTTCCTCACGAGAAGGCCGCGCATGTTCTCACCTATGAAGACCATGATGGAGACTGGATGATGGTTGGGGA
upper sequence: LOC_Os01g18360.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0005g02550.t01 (Vitis vinifera), 3'ss of exon 3
taattcaattttcatgtggtccaatctcacctcgtcatgatatacacatggcgatggttgtcgggtgttgtatataatcatatatgtttgata--tgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA------------
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------------------------------------gtaagtcccacatatttctgttgat---gtgctctagtcaatcagaaatcattaatgactcatttcaagcagGGGCTGAGGTGG------ATGGAGTTCTGCATTCTGAGAAATGCCATGTGCTAACATATGAAGACAAGGAAGGAGACTGGATGATGGTTGGGGATGTTCCTTGGGAMapped 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|89185778|gb|CI047647.1|CI047647EST: TGACAGCCTCCTCATCAAGCTCTGCCACATGTTCAAGACGCCCATCACCT ATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCC
genomic: TGACAGCCTCCTCATCAAGCTCTGCCACATGTTCAAGACGCCCATCACCTgtaagtatgc ... atatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatggcgatggttgtcgggtgttgtatataatcatatatgtttgatatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA
gtttgat putative branch site (score: 5)
tatataatcatatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattcaattttcatgtggtccaatctcacctcgtcatgatatacacatggcgatggttgtcgggtgttgtatataatcatatatgtttgatatgattagATGCTGATGTTATGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA