Sequence
atgc intronic sequence ATGC exonic sequencegttaataatcatcaaaactcgaggggagttggcacaaccacattatttcatcttgaactacactaaatattctacttttattttgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTTTCATAGCCTTTGGTGACATTCTTGACTTACACAAAAAGTTCCTTGAACT
Basic information
| species | Oryza sativa |
| transcript | LOC_Os05g01700.1 |
| intron # | 16 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 18
gttaataatcatcaaaactcgaggggagttggcacaaccacatta--tttcatctt--gaactacactaaat--attctacttttattttgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTTTCATAGCCTTTGGTGACATTCTTGACTTACACAAAAAGTTCCTTGAACT
||| || || |||||||| | || | || |||||| || |||||| || | | |||| ||| | | ||| || || ||||||||||||||||||||||||||||||||||||| || || |||||||| || ||||||||||| || ||||||||||| ||||| || ||||||||||||||
gttgctactcttcaaaacttttcc--atttttccaaaatacattagtttccatcttatgagcatccggaaatgcatttttcctttgcttcgtgcaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCTTCAGTGGTGTCACAGAGCTTCATAGCCTTCGGCGACATTCTTGAGTTACATAAGAAGTTCCTTGAACT
upper sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 18
gttaataatcatcaaa-actcgaggggagttggcacaaccacattatttcatcttgaactacactaaatattctacttttattttgtac-aacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTTTCATAGCCTTTGGTGACATTCTTGACTTACACAAAAAGTTCCTTGAACT
| | | | | | || | | | | |||||| ||||| | | || || || | ||| || ||| ||| |||||||||| ||| |||| |||||||||||||| || ||||| || |||| || ||||| |||||||| || || | |||||| | |||||
----------gtaagatatttgcattgaatcatt-tactctctatatttc-tcttg--ttgctctcctctctcacagacaatactatactaatagGTGAGCTGGCACATGCACTGAGGTTTTTGGCATCTGTTGTTTCTCAAAGCTTTTTAGCTTTCGGTGATATTCTTGAATTGCATAGAAAGTTTGTAGAACTMapped 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|88332517|gb|CI651677.1|CI651677EST: GTTATATGCTCTAGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAG GAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
genomic: GTTATATGCTCTAGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAGgttaataatc ... tgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
EST:
gi|300216062|gb|HO088688.1|HO088688EST: GTTATATGCTCTAGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAG GAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
genomic: GTTATATGCTCTAGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAGgttaataatc ... tgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
EST:
gi|29685003|gb|CB681278.1|CB681278EST: AGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAG GAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
genomic: AGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAGgttaataatc ... tgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
67 (upstream exon),
75 (downstream exon)
Score:
16GATTTTGTAACAAAGCAACTCCCTCACAATGTAACATGGGGTCTTAGTTTGTTATATGCTCTAGAGCACAAGGGTGACAGAGCTTTGACTTCAACTCAAGgttaataatc ... tgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTTTCATAGCCTTTGGTGACATTCTTGACTTACACAAAAAGTTCCTTGAACT
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattatttcatcttgaactacactaaatattctacttttattttgtacaacagGAGAGTTGGCACATGCTCTGCGGTTCTTGGCATCTGTTGTGTCACAAAGTTTCATAGCCTTTGGTGACATTCTTGACTTACACAAAAAGTTCCTTGAACT
cactaaa putative branch site (score: 16)
ttctacttttatttt putative PPT
taaatattctactttt TA-rich tract
