Sequence
atgc intronic sequence ATGC exonic sequenceAAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtcatccttcgattgtatagtttttaaaacttg...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G021849_T01 (Zea mays), 5'ss of exon 3
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtcatccttcgattgtatagtttttaaaacttg------
||| ||||||| |||||||| ||||||||| | ||||||||||| |||||||| |||||||| ||||| ||||||||||| || || || ||||| ||||||| | |||| ||| | |||||| || | | |||| ||| | || || | | | | | | | | | || || |
AAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGACATCCCTCATGGATACATTTGGAGTCCTCATCTAGTCCCGAAACCAAAAGgtttgctgtatctattggctagagctgaaagttg-gcaatttaccttgtcat----tcttttcccatattaattccaaagcatgtgggtct-gaatctcgatcttt
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 6
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaatttatatgttatcccttttcacgtcatgcttaaccttgtca-tccttcgattgtatagtttttaaaacttg-----
||| ||||||| |||||||| ||||||||| | ||||||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| ||||||| || |||| ||| | | | || |||| | | | || ||||| || || | | | | | | | | | | |||| ||||
AAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGACATTCCGCATGGATACATTTGGAGTCCTCATCTTGTTCCGAAACCAAAAGgtttgccatatctattggctagagccggaagttatgcaatttacttt-----gtcattttttcccatattagttcccaaagcatgtgggtcttaat-cttgacctt
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaa--tttatatgttat---cccttttcacgtc---atgctta----accttgt---catccttcgattgtatagtttttaaaacttg---------------------------------------------------------------------
||| | || || | || ||| | |||||| | ||||| || ||| | ||| || || || ||||||||||| |||||||| |||||||||||||| | | | | | | |||| | || | ||||| | | || | ||| | ||| | | | |||| |||| || || || || ||
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcg-aactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacagMapped 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|13165000|gb|AU173797.1|AU173797EST: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG ATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
EST:
gi|42793914|gb|AB117813.1|AB117813EST: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG ATTGGGGCCCCAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
EST:
gi|58670931|gb|CK059617.1|CK059617EST: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAG ATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
genomic: CATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTT
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:
64 (upstream exon),
71 (downstream exon)
Score:
20AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatg ... tctgttgcagATTGGGGCCCTAAGATTGATGTTGTTGGATTTTGCTTTCTTGATCTTGCTTCCAATTATGTGCCTCCTGAACCACTTGTAAAATGGCTTGAAGCTGGTGA
<
<
<