Sequence
atgc intronic sequence ATGC exonic sequencegtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g37960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110143_T05 (Zea mays), 3'ss of exon 2
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG-----
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gtcaggcgtcggtttgaattctcgggccggt-gcttcgatgactgtttcctcacgcttcgtttgtcgg------tgtcctcgc-----agGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGT
upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110143_T01 (Zea mays), 3'ss of exon 2
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG
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gtcaggcgtcggtttgaattctcgggccggt-gcttcgatgactgtttcctcacgcttcgtttgtcgg------tgtcctcgc-----agGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG
upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G016296_T06 (Zea mays), 3'ss of exon 2
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG
|| ||| | | ||| | ||| | | |||| | | | ||||| || || ||||| || || | | ||||| |||||||||||||| |||||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||
gtcaggcgtccgtttcaatttccgggccggtggttc-gatggctgtttcctcagg----ttttg--------ttcgtcggtggctcgcagGACCGGGGACTCGAGGGGTTTCGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG
upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110143_T03 (Zea mays), 3'ss of exon 2
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG--------------------
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gtcaggcgtcggtttgaattctcgggccggt-gcttcgatgactgtttcctcacgcttcgtttgtcgg------tgtcctcgc-----agGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGTTTTTTTTTTCGACTGMapped 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|88726297|gb|CI749952.1|CI749952EST: TTCGACCGCTACGGCAAGGTCGTCGACGTCTTCATCCCGAGGGATCGGAG GACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGA
genomic: TTCGACCGCTACGGCAAGGTCGTCGACGTCTTCATCCCGAGGGATCGGAGgtgaggagcc ... cgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGA
EST:
gi|33794171|gb|CF322976.1|CF322976EST: TTCGACCGCTACGGCAAGGTCGTCGACGTCTTCATCCCGAGGGATCGGAG GACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGA
genomic: TTCGACCGCTACGGCAAGGTCGTCGACGTCTTCATCCCGAGGGATCGGAGgtgaggagcc ... cgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG
aaaattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG