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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttacc-ctatgctcgctcttatttcctgttgttgatcactgctgcctga--tctgacctgtataattattcttgcag
|||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| || ||||| |||||||| ||||||||||| || | || | || | ||     || ||||||| | | | || |   |  || |||   ||| |||||||       |     ||
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTCAACCCTGAGAGGACCATCTTTGACGTCAAGCGTCTCATCGGAAGAAAgtagtgcctctctcccacaattgcttctattatttcgtctcgctg-tgggttatgtctggcgtcttacctgtaatgcccattgcttag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatt--------tcctgttgttgatcactgctgcctgatctgacctgtataat----tattcttgcag
||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||| || ||||| |||||||| ||||||||||||   | || |  ||||   |  ||  | ||        ||  ||||| | | | | ||| | |   | || |   ||||     |||  |  ||
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCCGTCAACCCTGAGAGGACCATCTTTGACGTCAAGCGTCTCATCGGAAGAAAgtaacacctctct--cctacagttacttctgttgaatttcgtctcgttgtgggttatttctggc-gtcttaactttagtaatgccccatttatttag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| || ||||| ||||| || |||||||||||||| | ||||||||| |||||||| |||  |||||| ||||||||  | || ||||||||||||||| | ||   |  |   |  | | | |||   |   ||| |  |   ||       |  || |    ||   |  | ||||||
TCACCGACAGTGAGAGACTCATTGGGGAGGCTGCCAAGAATCTGGCAGCTGTCAACCCAGAAAGGGTCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaa-gacatcct--caagtttttgat-ttaggacaatttgat--ttgatgtgaataaaggtgtctgacatgtatccttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggc-actttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| || ||||| || || || |||||||||||||| | ||||||||| |||||||| ||||||||||| ||||||||  | || |||||||||||||||     |||  |    ||  | |    | |    || ||  ||||| || || ||||          ||   | || ||||||
TCACCGACAGTGAGAGACTAATTGGAGAGGCTGCCAAGAATCTGGCAGCTGTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagacttactcaagttgatttttgacaatttgatttgatgg-gatcaatggtgactgac---------atttatctttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctat-gctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| || ||||| ||||| || |||||||||||||| ||||||||||| |||||||| ||||||||||| ||||||||  | || || ||||||||||||       | |   | | | |   |   | ||    ||| ||    |   ||      ||||| || ||     || ||||||
TCACCGACAGTGAGAGACTCATTGGGGAGGCTGCCAAGAATCAGGCAGCTGTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATCGGAAGAAAgtaagacttgctcaagttgttgatttttgacaatttgatttggtgggatcaattgtta---ctgacttgcatc----tttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| || ||||| || || || |||||||||||||| | ||||||||| || ||||| ||||||||||| ||||||||  | || |||||||||||||||       |||| | |   | | |  | |||     | |   |   ||    |     ||||    ||   |  | ||||||
TCACCGACAGTGAGAGACTAATTGGAGAGGCTGCCAAGAATCTGGCAGCTGTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaa----gacttactcaag--ttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttg-cag
| || ||    || || ||||| ||||||||||| ||||| || |||||||| || |||||||||||  ||||||| || ||  |  | || ||  |||||||||  |   |||  || ||       || ||||   |||  ||| | |  ||   | |     || | | ||| |  ||| |||
TTACTGACTCTGAAAGACTCATTGGTGAGGCTGCTAAGAATCAAGCAGCTGTTAATCCAGAGAGGACTGTCTTCGACGTTAAGAGATTGATCGGGCGAAAgtaattac---ttattctctgt----gtttgtttcaccttggagatga-tattgttggtttaagtctttgttattgtatttggcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttg-cag
| || ||    || |||||||| ||||||||||| ||||| ||||| ||||| || || ||||||||  ||||||| || ||  |  | || ||  |||||||||  |  | | | || |  |  ||  ||| |  |  || |||| | || ||  | |  |   || | | ||| |  ||| |||
TTACTGACTCTGAAAGGCTCATTGGTGAGGCTGCTAAGAATCAGGCGGCTGTTAATCCTGAGAGGACTGTCTTCGACGTTAAGAGATTGATCGGGCGAAAgtaattac-ttattctcttttttttcttctatatgtttgtgatgat-attgttggtttaatt---ctttcttattgtatttggcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaat--ggcactttaccctatgctc---gctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttg-cag
|||| || || ||||| || || ||||||||||| ||||||||||| ||||| ||  | || ||||| ||||| ||||| ||  | || ||||||||||||||||  | |  | || |  | |||    |    |   |  | ||  |   ||  |     |   ||||    | |||| | | ||| |||
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| |  ||| | ||||| || || || || ||||| || || ||||| || || |||||||| |||||||||||||| || || |||||||| |||||| |  |  || || | |||    | |  || | | ||| |  | |||   |     ||  |                     
TCACCGAGACAGAGCGTCTCATTGGAGAAGCAGCGAAGAATCAAGCCGCTGTTAATCCCGAGAGGACGATCTTCGATGTCAAGCGGCTAATTGGAAGGAAgtaa-gttagattcccatttgcaatttttccttccttcttgatc-taactctcgtaccgtcatag--------------------

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 2
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag
||||||| |  ||| | ||||| || || || || ||||| || || ||||| || || |||||||| |||||||||||||| || || |||||||| |||||| |  |  || || | |||        ||||    ||  |  |   | || | |||||| ||     ||       |  |||
TCACCGAGACAGAGCGTCTCATTGGAGAAGCAGCGAAGAATCAAGCCGCTGTTAATCCCGAGAGGACGATCTTCGATGTCAAGCGGCTAATTGGAAGGAAgtaa-gttagattcccatttgca-------attt----ttcctacttgttccttcttgatctaactctcgta----ccgtcacag

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|29624638|gb|CB629649.1|CB629649
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|1631642|gb|C19371.1|C19371
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         A
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcag-
EST: gi|1631642|gb|C19371.1|C19371
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         A
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcag-
EST: gi|29630263|gb|CB635272.1|CB635272
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|88724502|gb|CI747761.1|CI747761
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|88730748|gb|CI754361.1|CI754361
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|58672968|gb|CK061654.1|CK061654
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|396941184|gb|HO188393.1|HO188393
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|29630765|gb|CB635774.1|CB635774
EST:     GTGAACCCAGATAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCACAGGGACATGAAACTTGTCCCC
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCC
EST: gi|29628702|gb|CB633713.1|CB633713
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|29630767|gb|CB635776.1|CB635776
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCACAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
EST: gi|86902315|gb|CI302346.1|CI302346
EST:     GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAA                         GTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT
genomic: GTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 297

TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcac ... attcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGATTGTGAACAAGGACGGTAAGCCCTACATTCAGGTCAAGATCAAGGATGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA