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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttattttaacttttcttacttatgcatcagcaagtttttctcttgtatgttcattgttgtgtagcacacactcttgcctgttggtatgtttaag...

Basic information

species Oryza sativa
transcript LOC_Os10g38970.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G162292_T01 (Zea mays), 5'ss of exon 3
GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttattttaacttttcttacttatgcatcagcaagtttttctcttgtatgttcattgttgtgtagcacacactcttgcctgttggtatgtttaag------
| ||||| ||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||||     |||| |   ||| || ||  ||   ||    ||| |   |   |   || ||  | |  ||  |   |   ||||   ||| | | ||          
GTTGGGTGAATCGCTTTGCCAATGCCGGTGATACTGCTGTGGTTGTTGCTGAGAACACAGCAGTTAAGgta-----atttcagaatttgttgct-gtgatacaatgtgttatctccaatttgcttaatcctagcataaaatttatgattgctccttgcttttttattatttttc

upper sequence: LOC_Os10g38970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G24630.1 (Glycine max), 5'ss of exon 3
GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgc--ttattttaacttttcttacttatg-catcagcaagtttt---tctcttgtatgttcattgttgtgtagcacacactcttgcctgttggtatgtttaag----------------------------------------------------------------------------------------------
| ||||||||| | |||||||||||||||||||| ||| ||| ||| ||||  || |||||| |   |||| |     | ||| |   | |  |||||||   |   |  || ||   | | || ||   | ||  |       |||     | || |||||  | || ||  |                                                                                              
GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaacaactttcaaaatccagacttatggtcttgtcttgtgttaactattttatagaattatc-tcaccagtcaccacagcctggctgttcttgtgcttttggcttgaatgtttaaattacatagttattagtattggcatatcttgagaaactctatgtatgattgccctgatgatcataccctggccattgcag
















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|33816213|gb|CF333954.1|CF333954
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|86510877|gb|CI153510.1|CI153510
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|33804321|gb|CF328035.1|CF328035
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|29682951|gb|CB679226.1|CB679226
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|3761045|gb|C98299.1|C98299
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACNCAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|6850181|gb|AU082300.1|AU082300
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACNCAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|87016828|gb|CI284162.1|CI284162
EST:     GCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: GCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|88986336|gb|CI033581.1|CI033581
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|88977233|gb|CI024970.1|CI024970
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|33814559|gb|CF333144.1|CF333144
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAANTAGTCAATGCCAGTAGAGTAGCATACAG
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAA-TAGTCAATGCCAGTAGAGTAGCATACAG
EST: gi|86259224|gb|CI010525.1|CI010525
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|88835826|gb|CI370931.1|CI370931
EST:     AGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: AGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|163920984|gb|EG710397.1|EG710397
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|33817057|gb|CF334367.1|CF334367
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TNTCAGACAGGCTAAAACAGAAATAGTNCAATGCCAGTAGAGTAGCATACA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagT-TCAGACAGGCTAAAACAGAAATAGT-CAATGCCAGTAGAGTAGCATACA
EST: gi|88243897|gb|CI243019.1|CI243019
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|33662689|gb|CF293656.1|CF293656
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|218505580|gb|FG966210.1|FG966210
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|86888041|gb|CI297858.1|CI297858
EST:     CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: CCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
EST: gi|55410674|gb|CV723050.1|CV723050
EST:     TGCTGAGAACACAGCAGTTAAG                         TTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA
genomic: TGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGA

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: 57 (upstream exon), 45 (downstream exon)
Score: 20

GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttat ... tgttttgcagTTCAGACAGGCTAAAACAGAAATAGTCAATGCCAGTAGAGTAGCATACAGATTTATGGCAGGCCTGGCATCGAAAAATCAAAACCCACAACCAGAGTCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgcttattttaacttttcttacttatgcatcagcaagtttttctcttgtatgttcattgttgtgtagcacacactcttgcctgttggtatgtttaag

- - - - - - - - - -  ATGCTG