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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtgtttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT

Basic information

species Oryza sativa
transcript LOC_Os01g10290.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G112278_T01 (Zea mays), 3'ss of exon 2
gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtg-tttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT------------
                           |     | |||  |||  ||  | |  ||  | | | |  |  |  |  | | |||| ||  | | |||||| ||||||||||||||||||||||||| || || ||   ||||||||| ||||| || || || || || |||||| |||| |  ||||| |||||| ||| |||             
---------------------------gtaatattcctttatg--caccacccttatttttttgtcctcaccagtttctgacttctggctccccttttgaacaggtaccttttcatatttttgaaattcatagCGATAGTCATACCGACTATCGAGTACGATTATACAATGGACGTCGACCGTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G490260_T01 (Zea mays), 3'ss of exon 1
gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtg-tttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT
                           |     | |||  |||   |  | |  ||  | | | |     |  |  | || ||| ||  | | |||||| ||||||||||||||||||||||||| || || ||  |||||||||| ||||| || || || || || |||||| |||| || ||||| |||||| ||| ||| 
---------------------------gtaatattcctttatg--taccacccttatttttttgtccccaccagtttctatcttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCAACTATCGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 8
gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtg-tttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT
|||||||| | |   |    ||| ||   |  |  ||        |     |    |             |  |  | |||||| ||  | | |||||| ||||||||||||||||||||||||| || || ||  |||||||||| |||||||| || || || || |||||| |||| || ||||| |||||| ||| ||| 
gtaatattcttttatgcaccaccctt-attccccccccccccccccccctcccccccccacacacacacaccagtttctaacttctggctccccttttgaacagGTACCTTTTCATATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTG

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|29638207|gb|CB643216.1|CB643216
EST:     AAGATCATTGATGTTTTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88830849|gb|CI079283.1|CI079283
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88226114|gb|CI226030.1|CI226030
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|86870218|gb|CI319324.1|CI319324
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|55440203|gb|CV733411.1|CV733411
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATAT
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATAT
EST: gi|89194317|gb|CI116754.1|CI116754
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|86838969|gb|CI330376.1|CI330376
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GCACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88220871|gb|CI218722.1|CI218722
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88290160|gb|CI550382.1|CI550382
EST:     ATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: ATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|86889035|gb|CI314651.1|CI314651
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTG
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATA-TTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTG
EST: gi|86488895|gb|CI131528.1|CI131528
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|86497450|gb|CI140083.1|CI140083
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|29686213|gb|CB682488.1|CB682488
EST:     AAGATCATTGATGTTTTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|87015628|gb|CI277586.1|CI277586
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88323392|gb|CI553637.1|CI553637
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
EST: gi|88489074|gb|CI426345.1|CI426345
EST:     AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAA                         GTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA
genomic: AAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGA

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: 70 (upstream exon), 48 (downstream exon)
Score: 14

CAGGCAAGCATGCTTCAGTGCATCCATGCAAACATGCTGCTGTGATGAAAAAGATCATTGATGTTCTAATGTCTCAAGGAGTTGAACCAGAAGTTGACAAgtaatattat ... ttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcagtacatctctttgttggctggcctgtaacttgtgtttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT
                           ctgtaac  putative branch site (score: 14)
                                 cttgtgtttctctttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattatctacagagataccttttgctgactgcctggatgatcaaaagcagtacatctctttgttggctggcctgtaacttgtgtttctcttttggacagGTACCTTTTCATATTTTTGAAGTTTATGGCCTCAGTCATACCCACTATTGAATATGACTACACTATGGACTTCGATCTGGGCAGCACAAGCAGATGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG