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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaaactggaactaggttattacgttacattattacgaactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG

Basic information

species Oryza sativa
transcript LOC_Os02g10720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G497531_T01 (Zea mays), 3'ss of exon 2
accaaactggaactaggttattacgttacattattacg----aactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
    |||      | | | ||| | | |  ||  || |    | | |||    ||     |||| | |||  | |  ||   |     | |||||||| | |||| ||||| || ||| |||||||||| || |||||| |||||||  |||| || ||||||||| ||||||||  || ||  |||||||||||
---gaaccactggtggttcattgcctcatttttatatgctaaagcaataaaaccactaatggttca-ttccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G497531_T02 (Zea mays), 3'ss of exon 3
------------accaaactggaactaggttattacgttacattattacg----aactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
                |||      | | | ||| | | |  ||  || |    | | |||    ||     |||| | |||  | |  ||   |     | |||||||| | |||| ||||| || ||| |||||||||| || |||||| |||||||  |||| || ||||||||| ||||||||  || ||  |||||||||||
gtaggcgccgagggagaaccactggtggttcattgcctcatttttatatgctaaagcaataaaaccactaatggttca-ttccctgacattatgtccctcatttgtacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAAACGAAGACATAATTCTCAGGGTCAACAAAGTCAAGGACCAAAAATAAG

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G180967_T02 (Zea mays), 3'ss of exon 2
accaaactggaactaggttattacgttacattattacga-actatacgtacatgttaggttaagttcttttatgttg-attattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
 ||  |     ||| |  |  | | | |||| |||   | | ||||   |      | | |   |||  |  |  |   |   |  | ||| |||| | |||| ||||| || ||| |||||||||| || |||||| |||||||| ||||||  ||||||||| ||||||||  || ||| |||||||||||
tccggagaaatacttg--tggttcatcacatcatttttatattataataaagcaagatgcttcattcactggtactctgtcccttcatttgcacaaacatagGTCTTCTACTATGGCACCAGACTAGACAGCAGTGGATTGGAAACCGAAGGCTTAATTCTCAGGGTCAACAAAGTCAAGAACCAAAAATAAG

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G07210.3 (Glycine max), 3'ss of exon 2
accaaactggaactaggt-tattacgttacattattacgaactatacgtac---atgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG------------
      || || ||   | || |     | |||  |   |    | | ||    |  ||   ||   |   |  | | |||||||| |     |  |   | ||| ||||| || ||||||||||  |||| ||||||||||||||| |||||||   |   | ||    |||||  | |||| || | ||||||            
-ttttccttgatctgcatctactgtaggatatttctttcattcttgcatattttacatttttttgcatatctcca-gctgattattattacaatgta--tgcagGTCTTCTTCTCTGGAACCAGATGAGGCGACAGTGGGTTGGAAATAGAAGGCGTGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAGGTAAATAAATAT

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G07210.2 (Glycine max), 3'ss of exon 2
accaaactggaactaggt-tattacgttacattattacgaactatacgtac---atgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
      || || ||   | || |     | |||  |   |    | | ||    |  ||   ||   |   |  | | |||||||| |     |  |   | ||| ||||| || ||||||||||  |||| ||||||||||||||| |||||||   |   | ||    |||||  | |||| || | ||||||
-ttttccttgatctgcatctactgtaggatatttctttcattcttgcatattttacatttttttgcatatctcca-gctgattattattacaatgta--tgcagGTCTTCTTCTCTGGAACCAGATGAGGCGACAGTGGGTTGGAAATAGAAGGCGTGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAG

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G07120.2 (Glycine max), 3'ss of exon 3
-----accaaactggaactaggttattacgttacattattacgaactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
         | ||| | |||   ||  |  || | ||  | |   |  |   ||||| ||   ||   |   |  | | |||||||| |     |  |   | ||| ||||| || ||||||||||  || | ||||||||||||||||||||||||  |   | ||    |||||  | |||| || | ||||||
ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttc--ttgcatatctcca-gctgattattattgcaatgta--tgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAG

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|3766768|gb|AU030878.1|AU030878
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|12622897|gb|AU173110.1|AU173110
EST:     CCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: CCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|14192160|gb|AU184371.1|AU184371
EST:     GTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: GTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|86512046|gb|CI154679.1|CI154679
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|29689717|gb|CB685992.1|CB685992
EST:     TCACCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|8324561|gb|AU091706.1|AU091706
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|14192107|gb|AU184318.1|AU184318
EST:     AATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: AATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|88975725|gb|CI023976.1|CI023976
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCGAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|3766735|gb|AU030845.1|AU030845
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|88282037|gb|CI403433.1|CI403433
EST:     GAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: GAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|32947923|gb|BP184495.1|BP184495
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|88199489|gb|CI199339.1|CI199339
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|86853556|gb|CI329014.1|CI329014
EST:     CCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: CCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|4714360|gb|AU058327.1|AU058327
EST:     TTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|88984466|gb|CI015018.1|CI015018
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|86882289|gb|CI325747.1|CI325747
EST:     TGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGAGTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|86531003|gb|CI171209.1|CI171209
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|44678412|gb|CR291846.1|CR291846
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
EST: gi|88966152|gb|CI013028.1|CI013028
EST:     TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAG                         GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC
genomic: TCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGC

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: 58 (upstream exon), 69 (downstream exon)
Score: 50

CAATCTCAGCGTAGCATGTCTTCAATCAGTACGGCAGCACAATCGAGCGATCAGCATGGAGCTGGAAGTAGCACCAACCCAAATGAGTTTGTAAATCAAGgtaaaggcat ... acaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG
                          tgttgat  putative branch site (score: 50)
                     ttttatgttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaaactggaactaggttattacgttacattattacgaactatacgtacatgttaggttaagttcttttatgttgattattctacttgtacaaccgtagGACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG

accaaac
- - - - - - - - - - - - - - - - - - - - - - - gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacttg