Sequence
atgc intronic sequence ATGC exonic sequencegtaggaaaattgccctcatacctctaattttcctcattttgctggaaaagtaacacttctgtgcaatttagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g28180.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 13
gtaggaaaattgccctcatacctct-aattttcctcattttgct-ggaaaagtaacacttctgtgcaattt--agTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
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gtgatcatatcttcctccccttcctcaattttctccacgtttctcagagtggtaatgattctgttcaattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 14
-------------------gtaggaaaattgccctcatacctctaatttt----cctcattttgctgga--aaagtaacacttctgtg-caattt---agTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
| || | | ||| | |||||| | | ||||| | ||||| | || | | |||| || | || |||||||| || ||||| ||||||||||||||||||||| |||| |||
taatgtattccaataattttctgcaacttcatcatcagtgtttgaatttttgagctttgttttgacacaccaaagttaacctaatataattatttctcagCTTCGAGAATCAAAGGGAATGACAACAATCAAATTCCGTCCACATTCTGGAGAG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 13
----------gtaggaaaattgc-----cctcatacct----ctaattttcctcattttgctggaaaagtaacactt----ctgtgcaatt------tagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
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agtaatgtattcaaagaattttctgcaacttcataatcggtgttgagtttttgagctttgtttgacacaccaaagttaaccctatataattatttttcagCTTCGAGAATCAAAGGGAATGACGACAATCAAATTCCGTCCACATTCTGGAGAGMapped 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|33796571|gb|CF324153.1|CF324153EST: TTTCATATTATGCATATTACTGCTATGCTAACTTATACACACTCAATAAG TTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGC
genomic: TTTCATATTATGCATATTACTGCTATGCTAACTTATACACACTCAATAAGgtaggaaaat ... tgcaatttagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGC
EST:
gi|58687285|gb|CK075972.1|CK075972EST: TTTCATATTATGCATATTACTGCTATGCTAACTTATACACACTCAATAAG TTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCCACATGCTGG
genomic: TTTCATATTATGCATATTACTGCTATGCTAACTTATACACACTCAATAAGgtaggaaaat ... tgcaatttagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCC-ACATGCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catacctctaattttcctcattttgctggaaaagtaacacttctgtgcaatttagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
aagtaac putative branch site (score: 2)
cttctgt CT-rich tract
tctaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggaaaattgccctcatacctctaattttcctcattttgctggaaaagtaacacttctgtgcaatttagTTGCGTGAATCAAAAGGGATGACCACAATCAAATTCCGTCCACATGCTGGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG