Sequence
atgc intronic sequence ATGC exonic sequence...aaattatgttgccaatacctttttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52900.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 18
aaattatgttgccaatacctttttctatcttggttttg-cgctttatatt--cttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
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--tttaatccagtgatgcctttgtattttttaatactggcgcactgttttaacttgctactgtacattaacaa-ataatgcatttggttatgctttctatcagGGAGGCGATCTGACAGAGATTGGTGAAAGAGGAGTTAATATTAGTGGAGGGCAGAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATG
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 20
aaattatgttgccaatacctttttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
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--------------gtaagattgtttataa-aatgtcatcttctctaaactaat----gggaattttctttttataatcatctcatttatatcttctcagGGACGTGATTTTACAGAGATCGGAGAAAGAGGAGTCAATATTAGTGGTGGTCAAAAGCAAAGAGTTTCCATAGCTAGGGCTGTATACTCAAATTCGGATA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
lower sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
--aaattatgttgccaatacctt----tttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
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gtaagttttgaggagagcttcgtggagttgataacaaggatttgtcttgcctgttctcgtgttgctaagtttgtttcaacctct---ttctcttgcttaat---agGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 18
lower sequence: AT1G30400.2 (Arabidopsis thaliana), 3'ss of exon 18
------------------------------------------------------------------------------------aaattatgttgcc--aatacctttttctatcttggt--tttgcgctt-tatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttg-ttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
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gtaagttttgtggagagttacttagccatgtgcattgaaaatttcctgaggtgaaacgaaccttgaaatctgttggtgcgatgtaaatcgaaaaaactgaattgcatcagttctgttgatagcatgtacttctattttctagtgctcaggtatcta-agcttgtttcctcttctttctcttgattgatagGGAGGTGACCTCACGGAGATCGGAGAAAGGGGTGTTAACATCAGTGGGGGACAAAAGCAGAGGGTTTCTATGGCTAGGGCCGTTTACTCAAATTCAGACGMapped 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|157650622|gb|EX450256.1|EX450256EST: AGAAAGCAATAGATGTCACTTCATTACGGCATGACCTTGACTTACTCCCA GGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGA
genomic: AGAAAGCAATAGATGTCACTTCATTACGGCATGACCTTGACTTACTCCCAgtaagttcta ... ttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
aattgac putative branch site (score: 3)
aaaatatatcttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattatgttgccaatacctttttctatcttggttttgcgctttatattcttgtacctgcaaattgacaagaaaatatatcttcttatgcttgttgtcagGGTGGTGACCTAACAGAGATTGGAGAAAGAGGAGTTAACATTAGTGGGGGACAAAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG