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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g62420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 6
gtattccttctaacata-gagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcct-ggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacatt--agGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG
||||  ||||| |   | ||||||| ||  || ||||      ||   | ||||          || || |    |    | ||     | | |||   |   |||||||   |    | | || |    |    ||||||| |  |  | || |||||| || ||||||  |||  ||||||||||||||||||||||||||||     | |||||||| ||||||||||||||||  || ||||| |||||  |||
gtatagcttcttatgcacgagcaataactgcatgatt------ttttttccaca----------tcgtagatagtt----gcttccatttgtgtctcccggtattcttgatttacatatcgatatcaatgttcttaattctgctt-tgtgtatcatttgagatgtgcatggtattgtagGTTCATGATGGTCTGAGAAAGTGGCTCCACTCCAATGTTAGCCCTGCAGTTGCTGAATTGACAAGGATAATTTATGGAG
















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|29669431|gb|CB665706.1|CB665706
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|27576926|gb|CA999620.1|CA999620
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|58679577|gb|CK068264.1|CK068264
EST:     TTTGGGCCATTGGAACCGGCCAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGC
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGC
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTG
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTTTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|58674808|gb|CK063495.1|CK063495
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GATCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT

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: 69 (upstream exon), 73 (downstream exon)
Score: 23

AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG
 acctgat  putative branch site (score: 23)
                            aattatttgaaatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTTGCTGAATCAACCAGGATTATTTACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG