Sequence
atgc intronic sequence ATGC exonic sequencegtatgattgtttaattgtttacagtgcaacgtatgatgctatattcctaacttccacagctaacattttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g51480.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
--------------gtatgattgtttaattg-tttacagtgca--acgtatgatgctatattcctaacttccac--agctaac----attttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
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gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgtt-gagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
-----------------gtatgattgtttaattgtttacagtgcaacgtatgatgctatattcctaacttccac---agctaac-attttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
|| || | | ||| ||| | | | | || | | ||||| | ||| | | || | | |||| |||||| |||||||| ||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| || |||| |||| || ||||
gtgagtcttttttaactgt-tggcgatcttattatttgtatttttcttttttgtgtca-gtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------gtatgattgtttaattgtttacagtgcaacgtatg----atgctatattcctaacttcc--acagctaac---attttttttcctgtttgagc---------agCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
||||||| || | | || ||| || || ||| || ||| | | || || | | |||| | | || | ||||||||||| ||||||| || ||| ||| |||| || |||||||||||||||| ||||||||||| || |||| || ||||| | || | || |
gtaaaacgttttggatacgaaattgtttttccgtctttatatgaatacatgccaaatcttagattgttatgttcacaagaactcaccggactcttttgattatctgtgtttgttttaaagCACGAGGAAGGTGCGATCGAGGAGAGAGCTCGGGACTATAATGCAAACTGGATGACGGCAGTTGAGATACTCAATGATGACATCTACCTCGGTACTGATA
upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
gtatgattgtttaattg--tttaca-gtgcaacgtatgat--gctatattc-ctaacttccacagctaacattttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
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gtataacttctagacgaaatttgtgtgtttaaaaactgatctactatgttcatttggtattgtttctgatggcttattcttgaatgtaaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGAMapped 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|29669279|gb|CB665554.1|CB665554EST: TCATTGTAGTTGGAGACTTGATGAAATCAATATCCTTGCTCGTGTACAAG CACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTAGTTGGAGACTTGATGAAATCAATATCCTTGCTCGTGTACAAGgtatgattgt ... gtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGG
EST:
gi|87017593|gb|CI289726.1|CI289726EST: TCATTGTAGTTGGAGACTTGATGAAATCAATATCCTTGCTCGTGTACAAG CACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTAGTTGGAGACTTGATGAAATCAATATCCTTGCTCGTGTACAAGgtatgattgt ... gtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgatgctatattcctaacttccacagctaacattttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
cattttttttcctgtt CT-rich tract
taacatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattgtttaattgtttacagtgcaacgtatgatgctatattcctaacttccacagctaacattttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG