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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgatttattataatctaagataagatggtttacatctaggcttaggttgctgctgagtttcatctgaagttctttcaaattatcaatcacttgcatgtacttgttacttcttttttacag

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 10
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgat--ttattataatctaagataagatggtttacatctaggcttaggttgctgctgagtttcatctgaagttctttcaaattatcaatcacttgcatgtacttgttacttct-tttttacag
|| |||||||||||||||||||||||||| |||||||||||||||||||||||||  ||  |||| || || ||||| |||||||||||||||||||||||||| ||||||   || |||||  | | || ||  || || | || |    | |    || |||||| | | | ||||  ||| | ||||   | |     ||  | |  |||| || |         || || ||| | || |||||||||
GGGGAAGCTCTCTTTCAAACACATGAAAACTTGGAGCATTTGGCTATGATGGAGAAGGTCTTAGGGCCTCTCCCAAAGCATATGATTGTCAGAGCTGAgtatgtgtacaagtcttttgttatcttcttatcatactttttgtcatttttattta---tgtatacatccaagatgaggtatctgatcagttctgttt-----tcgcttatcttattaacc---------tatttattaatgctgtttttacag

upper sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S425_6V6.2 (Physcomitrella patens), 5'ss of exon 10
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgatttat----tataatcta--agataagatggttta---catctaggcttaggttgctgctgagtttcatctgaagttctttcaaattatcaatcacttgcatgtacttgttacttcttttttacag--
||||| ||  | |||||||| || || ||| | ||||||||||||||||||||| ||||| | |||||| | ||    || |||||    || || ||||  |||  || | || ||||  || ||    | | |||    |    |||   | || |  ||  |||   || |    || ||  |     |     ||||||  | || |||    ||     |  ||  | |    |  | || | | |  ||||   
GGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGAgtgcgtac-catgatcctcgtattatttattggctctatcgactgcggtcttgtaaatgacttgcattaaatcaccatatctgagcctatgagtattaatcatcttcaattttttttttttgaactttcctgacttcctatgatcacctgtatcctacacag

upper sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 5'ss of exon 10
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgatttattataatctaagataagatggtttacatctaggc-ttaggtt---gctgctgagtttcatctgaagttctttcaaat-tatcaatcacttgcatgtacttgttacttcttttttacag---------
||||| ||  | ||||| || || || ||||||||||||||||||||||||||  ||||  |||||||  ||||   ||| |||||    || || ||||| ||  ||| |    |  | ||  |||| ||  ||  | || |||||  |    || | |  ||  || |   | |||   | |  ||| | | |   || ||| | |  | | | ||    | |  | | |  ||         |||  ||           
GGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGAgtaagtg-acatgcgtctgttaatcttttcttggcttcctctattctaatcttgtgtgatgtgtattgagccaccaagtttgagttcatgattatgagtagacgttttctatattctgtctgaaagtgtcctttggtttacgagcactttcaacgacctctgcag

upper sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 5'ss of exon 12
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtc-ttcgttatagttt-catgatttattataatctaagataagatggtttacatctaggcttaggttgct---gctgagtttcat-------ctgaagttctttcaaattatcaatcact-tgcatgtacttgttacttcttttttacag-------------------
||||| || || ||||| || ||||| || |||||||||||||||||||||||| | ||| |||||||| ||||    || |||||    || || ||||| || |      |  ||   | || ||| |   | ||| | |   |||   |  |  ||||||| |   ||  |||  || |   ||||||||   |        | | ||| |  | | |  | |||  || || |  |   | || ||    | ||  |                    
GGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGAgtacgttttttttcttgttaactttattttgcccaaattactttgg-ctatcct--gtcggtttacttaatggtatagagtggtcacgctgagttctgtgcgtatgttaaggttttaccgactagtaaatgtctatggactttaatattgctaacatgttgtatggattacacaaatattcag

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|27577533|gb|CB000228.1|CB000228
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|86419537|gb|CI054338.1|CI054338
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCCAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|88278121|gb|CI399121.1|CI399121
EST:     GTCCCCTTCCCAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: GTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|109712124|gb|CI104732.1|CI104732
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|88268204|gb|CI378139.1|CI378139
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|88278123|gb|CI399123.1|CI399123
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|88902914|gb|CI088452.1|CI088452
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|86434684|gb|CI105917.1|CI105917
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|27576166|gb|CA998860.1|CA998860
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|86484027|gb|CI126660.1|CI126660
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
EST: gi|86598138|gb|CI278528.1|CI278528
EST:     ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA                         TCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA
genomic: ATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGA

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), 50 (downstream exon)
Score: 11

GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatac ... ttttttacagTCGCCGTGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGAGGGGGCTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGAgtatgtatacaaggtcttcgttatagtttcatgatttattataatctaagataagatggtttacatctaggcttaggttgctgctgagtttcatctgaagttctttcaaattatcaatcacttgcatgtacttgttacttcttttttacag

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA