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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatcatgtgtttttactattcctccattttttctatcctgcgattcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT

Basic information

species Oryza sativa
transcript LOC_Os02g50880.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G144501_T01 (Zea mays), 3'ss of exon 8
agaatcatgtgttttta-ctattcctccattttttctatcctgcgattcaaaggggcccttagtttggctgacattact---taac-taatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT
     ||  | ||   | ||  |||    |   |   |   | |  ||  ||   |    |   ||   |||  ||| |   || | |||| |||||||||| ||||||||||||| ||||| |||||||| ||| |||| || |||||||||||||| || |||||||||||||| |||||||| |||||||| ||| ||||  
-----cacatattgaaaactgctccaaagtaactgtcaggattcttttttaattagtttctttattacttgaagttagtaactagcataatatatgatttgatagATTGTTGTCCTCGAGACGAAAACTGCAAAGTCTGCTACCCAGGACATTCTGACGACGCACTGTATACCGTCTGCAATGTCGGATGACCTTAAGGCCTAG-

upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 9
----agaatcatgtgtttttactattcctcc--attttttctatcctgcgattcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT
     |||  |    |    | ||    ||   ||| ||| |    ||  | | ||      | | |   | |     | || |    |||| |||||||||| ||||||||||||| ||||| |||||||| |||||||| || |||||||||||||| || ||||||||||| || |||| ||| |||||||| ||| ||||  
atgatgaaaaactgctccaaagtaactgtcaggattctttttgatttgttacttaacta---cttgaagctagt---aactagtagcataatatatgatttgatagATTGTTGTCCTCGAGACGAAAACTGCAAAGGCTGCTACCCAGGACATTCTGACGACGCACTGTATACCTTCTGCAACGTCGGATGACCTTAAGGCCTAG-

upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 8
---------agaatcatgtgtttttactattcctccattttttctatcctgcga-ttcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT
           ||  | |||   ||  ||        || || |||| ||| || || | | |    |||| |     ||| |||  || | |||  | |   |   ||||  || ||  |  |||| |  ||||| ||||| || ||    ||||| || || ||||| |||||||| || || |||||||||||||||||||| ||| 
aattaactatcaaataagtgaaattcttaccataaatttattgctatgctgtgaatttacatgaatgcttatt-----tgaaatt--ttgaataaccttt---tctgcagAAGGTAGTGTTGAAGACTAGCACTGCTAAGGCCGCAACCTTAGACATCCTCACCACACATTGTATACCTTCTGCGATGTCTGATGACCTGAAGACATAAA

upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 8
agaatcatgtgtttttactattcctccattttttctatcctgcgattcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT
        ||    || | || | ||| | |||| | | ||    |  ||| ||      |||   ||  | |||   ||||||||       |   ||||| || || |||   || || ||||| || || || || |  || |||||  ||||||||||||| || ||||||||||||||||| || ||| | | ||
--------gttcacttgccatccttccctgttttatgtgcttgtgtgaaaatgga-----agt--agcc-atattgactaactaatcctcttatatgcagATAGTGGTGCTTCGCACGAAGACTGCAAAAGCAGCTACTCTTGATATTCTTTCAACACACTGTATTCCATCGGCAATGTCTGATGATCTTAAGTCATGAT

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|163929409|gb|EG713834.1|EG713834
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|29642428|gb|CB647435.1|CB647435
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|218501871|gb|FG957167.1|FG957167
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88515656|gb|CI443310.1|CI443310
EST:     GTTTGATCTGGAGTATGACCAG                         ATTGTTNTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: GTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88676018|gb|CI730131.1|CI730131
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|86865124|gb|CI344614.1|CI344614
EST:     AGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: AGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|66914360|gb|CX101208.1|CX101208
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88906999|gb|CI376071.1|CI376071
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACACCACACTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88688423|gb|CI731999.1|CI731999
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|86875467|gb|CI323877.1|CI323877
EST:     TGAATTC-TGAAGTTTGATCTGGAGGATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|29622435|gb|CB627446.1|CB627446
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88845965|gb|CI084695.1|CI084695
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88531916|gb|CI458438.1|CI458438
EST:     ATTGCAAGGATGNATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: ATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88263098|gb|CI366872.1|CI366872
EST:     TGAAAATTGCAAGGATGAATTCTTGAAGGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TGAAAATTGCAAGGATGAATTCTTGAA-GTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|396941237|gb|HO188446.1|HO188446
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|58668496|gb|CK057182.1|CK057182
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|58681016|gb|CK069703.1|CK069703
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88481327|gb|CI418598.1|CI418598
EST:     TTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|88902416|gb|CI087954.1|CI087954
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
EST: gi|29632216|gb|CB637225.1|CB637225
EST:     TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAG                         ATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG
genomic: TTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTG

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: 67 (upstream exon), 71 (downstream exon)
Score: 25

TGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATGACCAGgtatccccag ... gatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT
                                  aactaat  putative branch site (score: 25)
                           attacttaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatcatgtgtttttactattcctccattttttctatcctgcgattcaaaggggcccttagtttggctgacattacttaactaatgtatgatttgacagATTGTTGTCCTTGAGACAAAAACTGCGAAGGCTGCGACACAGGACATTCTGACAACACACTGTATACCGTCGGCAATGTCTGATGACCTGAAGACCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - -catgtgt
- - - - - - - - - - -tcctcca
- - - - - - - - - - - - - - - - - - atcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaca