Sequence
atgc intronic sequence ATGC exonic sequence...atatctcattccttgttcttgacttttaatactactatcagcttggcaggttgctagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40010.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179810_T03 (Zea mays), 3'ss of exon 2
atatctcattccttgttcttgacttttaatactac-tatcagcttggcaggttgc-tagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
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-ttccattttttttatttttctttacaagcgggacgtacaaatcgagcgatttgcgctggctctgataaattgttgggt-tcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAG
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G071846_T01 (Zea mays), 3'ss of exon 2
----atatctcattccttgttcttgacttttaatactactatcagcttggcaggttgctagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
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agtgccaggccattcatcatgtttc-catccaccagcacttgcgttgcgctagct--ctgacttgtgtgttgtggctccttgct-tgacactctactcttccagGGATTGAGGCCAGGGGCTTCATATTTGGCCCGGCAGTCGCATTGGCTATTGGCGCCAAGTTCATACCTTTGCGCAAGCCTAGGAAGCTCCCCG
upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179810_T05 (Zea mays), 3'ss of exon 2
atatctcattccttgttcttgacttttaatactac-tatcagcttggcaggttgc-tagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG-------
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-ttccattttttttatttttctttacaagcgggacgtacaaatcgagcgatttgcgctggctctgataaattgttgggt-tcacttggacattcctgtccagGGATTGAGGCCAGGGGCTTCGTGTTCGGCCCGGCGATCGCGCTGGCTATTGGCGCTAAGTTCATACCTCTGCGCAAGCCAAGGAAGCTCCCAGGTGAGAGMapped 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|88211248|gb|CI210888.1|CI210888EST: CGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGCCGCCGTCGCCG GGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTG
genomic: CGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGCCGCCGTCGCCGgtaaacactt ... gtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaggttgctagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
agttaat putative branch site (score: 4)
tttgttt putative PPT
ttaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatctcattccttgttcttgacttttaatactactatcagcttggcaggttgctagttaatgtttcattcctggttgtgactttggtttgtttgaccagGGATTGAGGCTAGGGGGTTCATATTTGGCCCGGCGATCGCGCTGGCAATTGGCGCCAAATTCATACCGTTGCGTAAGCCCAAGAAACTCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - ttgttct
- - - - - - - - - - - - - - - - - - - cagcttg
- - - - - - - - - - - - - - - - - - - - - - - - ggttgct