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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCTTGGAGAGGTTCGATTACCTGCAGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcactatatcatcatgacaatctgtcttggatgttccaatggaaagaataaaacttgttgcttgcaccgttactatacatgtcactcagcttaagccctggttaacctaattcttgtgtgctcccctcattacag

Basic information

species Oryza sativa
transcript LOC_Os09g36670.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G158237_T05 (Zea mays), 5'ss of exon 2
AGCCTTGGAGAGGTTCGATTACCTGCAGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcactatatcatcatgacaatctgtcttggatgttccaatggaaagaataaa--acttgttgcttgcaccgttactatacatgtcactcagcttaagc-------cctggttaacctaattcttgtgtgct---cccctcattacag
 || ||| |||||||| |||||| ||||||||| ||||||| ||| | ||||| ||||||||||| ||||| ||||||||||  | |||  | ||  ||| | |    |||||||| |||||||||   |     || | |||||||||   ||  |  |  | |||||   ||||| |       | | |||  | ||||||||||        | ||| ||| |||
GGCGTTGCAGAGGTTCAATTACCAGCAGTTACTCACAGGGTCTACCTAGATGTAGAAATTGATGGCCAACACATAGgtatattgcaata--aacagtacattgt----tggatgtttcaatggaaatctttggtcacctattgcttgcattattttttcatgtttcactactcttaaccatcattacattgttggcttaattcttgttgatctgactcctaattgcag
















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|44665422|gb|CR278856.1|CR278856
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTCGAATTGTCATTGGCCTT-ATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88570043|gb|CI661218.1|CI661218
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCACAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88328504|gb|CI676714.1|CI676714
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88580780|gb|CI697732.1|CI697732
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTNGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|58597588|gb|CK008116.1|CK008116
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|58601241|gb|CK011769.1|CK011769
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|87005928|gb|CI289345.1|CI289345
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88419577|gb|CI686794.1|CI686794
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88307256|gb|CI641892.1|CI641892
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCACAAACAGTGG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88580485|gb|CI697419.1|CI697419
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88581910|gb|CI699127.1|CI699127
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|88335390|gb|CI650355.1|CI650355
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
EST: gi|58691487|gb|CK080174.1|CK080174
EST:     AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAG                         GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG
genomic: AGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG

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: 73 (upstream exon), 48 (downstream exon)
Score: 6

AGCCTTGGAGAGGTTCGATTACCTGCAGTTACTAACAGGGTATACTTGGATGTGGAAATTGATGGGCAACATATAGgtatatcact ... ctcattacagGTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG




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