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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g52490.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G171426_T01 (Zea mays), 5'ss of exon 1
-GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctc-tctctcgctggatgaatccttaccttgcag-----------
 |||| ||  |  | ||||| |||||||||||||| |  ||||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||||| || | |   |||||      | |   | |   ||||| ||| |   ||||   |  |  || | | |||||| ||  ||   | | | || | |             
CGCGGTCAG-TTGAACCATGGCGGACTCCAAGGCCACCTCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTGGCCCGCAAGCAATTCgtaagtggc--atccatcagaccaacatcttccaatcctt-ccgtcgatgctccccgtctcgtcccccatctctcactaaatctttgcctgccctccctctgtcttgcag

upper sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G151252_T01 (Zea mays), 5'ss of exon 1
-GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcag-----------
 ||||| | ||| | ||||| |||||||||||||| |  ||||||||||||||||||| ||||||||||||||||||||||| ||  ||||||| ||||| || || | |  ||||||      | | | | |   || || ||  |   ||||   |  |  || |  |||||| ||  ||   | | |  | | |             
TGCGGCTAGCTC-AACCATGGCGGACTCCAAGGCCACCTCGGCGGTCACCCTCCGCACTCGCAAGTTCATGACCAACCGCCTGCTGGCCCGCAAACAATTTgtaagtgac--gtccatcagaccaacaccttccaatcatt-ccatcggtgctccccgtctcgtccccatctctcactaaatctctgcctctcctccctcattcttgcag

upper sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 5'ss of exon 1
GCGGC-CAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcag----------------------------
 ||||    |||   |  |  | |   ||| ||| |     ||   |||| |||||||||| |||||||||||||||||||| ||  | |||||||||||||| |||| |  || | |      |  | || ||||||  |||    ||| ||  |||| |    |   | |     |       |  | |   ||                               
-CGGCATCGCTCGCTCGCTCACTGCAACCATGGCGGACAAAGCTTGCACCGTCCGCACCCGGAAGTTCATGACCAACCGCCTTCTGGCGCGCAAGCAATTCgtaagcgacgagttcgtc-----atttttttctcctctctgcaaggatgtctacgtgagttgcttgagtgttggatttttctcgtattgattatgggaagggcgttctgtttgtgtgtgttggcag

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|29685668|gb|CB681943.1|CB681943
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|66927289|gb|CX114137.1|CX114137
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|286327|gb|D15135.1|D15135
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|4716872|gb|AU057988.1|AU057988
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|38468914|gb|CF953045.1|CF953045
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|55436887|gb|CV731621.1|CV731621
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|29685667|gb|CB681942.1|CB681942
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|8857380|gb|AU094698.1|AU094698
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|4716870|gb|AU057986.1|AU057986
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|89167241|gb|CI252772.1|CI252772
EST:     CTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: CTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|29659093|gb|CB655368.1|CB655368
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG

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: 72 (upstream exon), 73 (downstream exon)
Score: 94

GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA