Sequence
atgc intronic sequence ATGC exonic sequence...tcaagggtttcttgctactgagattgatgaactaattaacagcttaattaatttactgagattcattgtctgatctgaaaatgaaaatacatcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g33940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G104074_T01 (Zea mays), 3'ss of exon 3
tcaagggtttcttgctactgagattga--tgaactaattaacagcttaattaatttactgagattcattgtctgatctgaaaatgaaaatacatcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGC---GAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
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------gtaacaagctagaggccttgtgttgtacacttctttaatttgtttctactagcagctggcaagttgtaaagcaactctgatgatctaat-ctgcagGAAGATGGATGGGTGGTATGTAGGGTTTTCAAGAAGAAGAACTATGAGCAGAGAGGCCACAACATGGCTGAGATGGCGGCACTGGACGACGATGAGCTCC---
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G041746_T02 (Zea mays), 3'ss of exon 3
------------------tcaagggtttcttgctactgagattgatgaac-taattaacagcttaattaatttactgagattcattgtctgatctg-aaaatga---aaat----acatcat-tgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTA---CCAGCGAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
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gtaataataaaggggcctttatatatatatcctgatctagtcctgtaaataccgttctttattttgtttcttgctagcgatcgagctgctgcaatgcaaagtgactcaaatcctgatatGGTCTACAGGAAGATGGTTGGGTGGTGTGTAGGGTTTTCAAGAAGAAGAGCTATCACCAGAGAGGCCTCAATCCGGCTGAAATGGCCGCCGCACTGGACG------------
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 3
------------------tcaagggtttcttgctactgagattgatgaac-taattaacagcttaattaatttactgagattcattgtctgatctg-aaaatga---aaat----acatcat-tgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTA---CCAGCGAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
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gtaataataaaggggcctttatatatatatcctgatctagtcctgtaaataccgttctttattttgtttcttgctagcgatcgagctgctgcaatgcaaagtgactcaaatcctgatatggtctacagGAAGATGGTTGGGTGGTGTGTAGGGTTTTCAAGAAGAAGAGCTATCACCAGAGAGGCCTCAATCCGGCTGAAATGGCCGCCGCACTGGACGACGACGAGC---Mapped 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|88377590|gb|CI605425.1|CI605425EST: ACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAG GAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGA
genomic: ACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatat ... atcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaatttactgagattcattgtctgatctgaaaatgaaaatacatcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
aaaatgaaaatacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaagggtttcttgctactgagattgatgaactaattaacagcttaattaatttactgagattcattgtctgatctgaaaatgaaaatacatcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGAGGCCTCAACCCGGCGGACATGGCGGCGGTCGACGACGACGACCTCCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - tgctact
- - - - - - - - - - - - tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaaa