Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgcatcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag

Basic information

species Oryza sativa
transcript LOC_Os12g01370.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G056546_T01 (Zea mays), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGG-GCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgcatcaatccatcga-gatctccatgaaaaacaaattgaaaatgcatgcaaacacag
           |  ||| | || |   |  ||||    || |  |    | ||||||||||| |||||||||||||||| ||||||||| ||     ||||| |    | | | | |  |    ||     || | || | |  | | | | | |    ||   ||  |  | || || | |||   |   ||  |                  
-----------GCGGTCGCTGTGGTACGTTGCGGTGGTGCTGGCCCTGGGAGCGGCGCAGGGGACCATGTTCTGGGCGCGCTTCGTCCTGGG-----ACTGGGA--CACGACTGACTGgtgtggcgtcgatatatattatattctcttttcgtcttcctatttttcttttaacgaactacttgatgcatgcatgcag-----------------

upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G354558_T01 (Zea mays), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttc--tattcattcattcatcgcttccatttcttttctcatatatgcatatatgcatcaatccatcgagatctccatgaaaaacaaattgaa-aatgcatgcaaacacag
 | |   |   |  | |   | |   |||||||  |||||||| ||||||||||||||||| ||||||||||||||||||||||| || || |||||||||||  | |     ||  || | |  |  ||   ||  |||  |    |  |  ||  |  |  |   |  ||| ||  | | ||  | ||  ||| |  |||       || |||
GCGCGGCGGCGGCGGGCATGGACAGTTGGGCGGTGTGGCCGCTGTACTGGGCGGCGCAGGGGACCATGTTCTGGGCGCTCTTCGTGCTGGGACACGACTGgtacgtacgtcgatctctcttcctccttttgttttgttttcttttctttcggttacgtatacaacgacgacgaaatgacgacgacgaccatgttgcatgatgttgatgcacgcag

upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccat---ttcttttctcatatatgcatatatgcatcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag
|  || |   ||  |  |    |  ||||   |  |||||| | ||||||  ||| || || |||||||||||||| |||||||| || || |||||||||||||| |  |  |  |  |    | ||   |   |  ||   |  | |  |  | | || |  | ||||| | ||    | || ||  |    ||  | ||| |          
CGGCTGGCGCTGCAGCTTTGAACAGCTGGTTTGTTTGGCCGTTGTACTGGCTGGCACAAGGAACCATGTTCTGGGCTCTCTTCGTGCTGGGTCACGACTGgtaattgcactaaaacctgttcgagattgagtgaatgtttaatttgtgtgaggctgtgtggacaattccat-gtgagagacgtggaatcc----tgtgagtgctt----------

upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgcatcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag--
|| |  |   ||  |       |  ||||   |  |||||| | ||||||  |||||| || |||||||| ||||| |||||||| || ||||| |||||||||||  || |         ||  |||        ||      | | ||| || | | | |       |  || |   |  |     ||||   |  | |  || |||     
CCGCCGGCGCTGCAGCTGTGAACAGCTGGTTTGTGTGGCCGTTGTACTGGCTGGCGCAAGGAACCATGTTTTGGGCTCTCTTCGTGCTGGGCCATGACTGgtaattg-tact---------ataacttgttcgagattgagaggacacgca-attttcgtgagaatgcgggaatgt---tagatgtggaattctgagagtagccagacatgcca

upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgc-atcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag
|  || |   ||    ||        |||   | |||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| ||||||||| || |  || |      |   |||   |||  |||||| |   | |   | |   ||||                                                  
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttt--tcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-------------------------------------------------

upper sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20170 (Selaginella moellendorffii), 5'ss of exon 1
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgcatcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag
|  || |   ||    ||        |||   | |||||| ||||||||||| || || ||||| ||||||||||| ||||| || |||||||| ||||||||| || |  ||   ||   ||   ||   ||  || ||     || || | | || ||||                                                  
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGCACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttctctcccagcaatgtttt---ttctttctcgatcttacgcgtctttg-atcag-------------------------------------------------

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|58680053|gb|CK068740.1|CK068740
EST:     GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTG                         TGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCA
genomic: GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttcta ... gcaaacacagTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCA
EST: gi|33684564|gb|CF312803.1|CF312803
EST:     TCCTCGGCCACGACTG                         TGGGCACGGGAGCTTCTCCGATAGCGCC-TGCTCAACAACGTCGTCGGCCA
genomic: TCCTCGGCCACGACTGgtaatttcta ... gcaaacacagTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCA
EST: gi|58664437|gb|CK053123.1|CK053123
EST:     GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTG                         TGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCA
genomic: GCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttcta ... gcaaacacagTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCA

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), 73 (downstream exon)
Score: 22

CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttcta ... gcaaacacagTGGGCACGGGAGCTTCTCCGACAGCGCCATGCTCAACAACGTCGTCGGCCACCTCCTGCACTCCTTCATCCTCGTCCCCTACCATGGATG




<











<


<