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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attattttatgggagaacttgagtttttcattgttctgatttgttgaatatgtatacattatctctcttaatatttataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G107867_T02 (Zea mays), 3'ss of exon 3
attattttatgggagaacttgagtttttcattgt-tctgatttgttgaatatgtatacattatctctcttaatattt-ataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
  |     ||  || || |  | | || | || | | | || | |  | |     |   || | |   ||  | ||| | |  | |||| || ||| ||||||| |||||||| || ||||||||||| ||||||||||| || || ||||| || ||||| ||||||||| |||| |||||||||||||||||||| ||||
-atggaggatacgacaattaaaatattcctttttcttttatatctaaattccaggtttgttttattagttgttttttcacattggaaaaattcatg-aacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGACCTAAAGCCGGAAAACTTGTTACTTGATTCAAAGTATAATGTAAAACTTG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
--attattttatgggagaacttgagtttttcattgttctgatttgttgaatatgtatacattatctctcttaat-atttataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
  ||  ||||||   |     | |   | | | | |||  |             | || ||||| | |   | | |   || || ||      | ||    |||| ||||| || || |||||||||||  ||||||||||||||||  | || || ||||| |||||||||||  |||| || || |  ||||||||| |||
gtatgtttttattttattttatcaacatgtaact-ttccaagcaaccattcgattttatattatatttgagagttaagaattagctacttggctttgatgtagATAATATCAGGAGTGGAATACTGCCATCGAAACATGGTGGTTCACAGAGACCTCAAGCCTGAAAACTTGCTTTTGGACTCTAAATGCAATGTAAAGATTG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 2
attattttatgggagaacttgagtttttcattgttctgatttgttgaatatgtatacattatctctcttaatatttataaggtaaaattttatggaaca---gATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
                                                |  ||   | ||  |    | || |    | |    || |   |   | ||   ||| || ||||| || ||||| || |||||||| ||||||||||||||||||||||||||||||||  || | || || || | ||  ||||| ||| |||
-----------------------------------------------gttcgtgctccttcgcctggtgaagaaaactgaatataactcgcacacatcaccagATCATTTCTGGAGTGGAATATTGTCACAGAAATATGGTGGTTCATCGTGATCTGAAGCCAGAAAATCTGTTGCTTGACTCTAGGTGCAATGTGAAGATTG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ17922 (Selaginella moellendorffii), 3'ss of exon 2
attattttatgggagaacttgagtttttcattgttctgatt-tgttgaatatgtatacattatctctcttaatatttataaggtaaaatt--ttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
       || | || ||    | | | || || || |  |    |||| | ||| |   ||||   || |  | || | | | ||   ||  |  ||| | ||||||| || || ||||| ||||| || ||||||||||| ||||||||||| || ||||| || || ||||| || |  || || |  | ||| ||| | |
------gtacgagaaaa---aaatgtctcgtttttttcttggcattgagtgtgtgt---ttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCGGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATCG

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10631 (Selaginella moellendorffii), 3'ss of exon 3
attattttatgggagaacttgagtttttcattgttctgatttgttgaatatgtatacattatctctcttaatatttataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
                              |  |  |||| ||  |       ||   ||   |  ||   ||  |  || || ||  ||       | || | |  ||   ||   ||  ||| | |   |||   |                                                              
-----------------------------gtCATCGTGATCTGAAGCCAGAAAATCTGTTGCTTGACTC--TAGGTGCAATGTGAAGATT------GCGGACTTTGGCTTAAGTAATATCATGCGAGATGGACACTTTC-------------------------------------------------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
attattttatgggagaacttgagtttttcattgttctgatt-tgttgaatatgtatacattatctctcttaatatttataaggtaaaatt--ttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
       || | || ||    | | | || || || |  ||   |||| | ||| |   ||||   || |  | || | | | ||   ||  |  ||| | ||||||| || || ||||| ||||| || ||||||||||| ||||||||||| || |||||||| || ||||| || |  || || |  | ||| ||| | |
------gtacgagaaaa---aaatgtctcgtttttttctttgcattgagtgtgtgt---ttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG

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|29663426|gb|CB659701.1|CB659701
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58679972|gb|CK068659.1|CK068659
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|33797130|gb|CF324430.1|CF324430
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATTATCTGGGGTTGAATACTGCCACAGAAACATGGGGTGGTTCATCGT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTAT-ATCTGGGGTTGAATACTGCCACAGAAACATGG--TGGTTCATCGT
EST: gi|33678911|gb|CF307150.1|CF307150
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|88250467|gb|CI348697.1|CI348697
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|33381730|gb|CF197073.1|CF197073
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|218488644|gb|FG955529.1|FG955529
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT

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: 74 (upstream exon), 72 (downstream exon)
Score: 74

ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatatgtatacattatctctcttaatatttataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG
                    tcttaat  putative branch site (score: 74)
            attatctctcttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attattttatgggagaacttgagtttttcattgttctgatttgttgaatatgtatacattatctctcttaatatttataaggtaaaattttatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGATCTGAAGCCAGAAAACTTGCTACTGGATTCAAAGTATAATGTAAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggtaaaa