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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttcataccctccttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccctgaccattttacattaaacttctttgttttag

Basic information

species Oryza sativa
transcript LOC_Os11g07910.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 2
TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttc---ataccctccttgattttatttacttttggaatgtgcatcaatgtatgttcctt---gcaact-aaccgattt-ccctgaccattttacattaaact----tctttgttttag
||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||||||| | |||||||||||  |||||| | |   ||| ||   | | ||||||  | ||| |||  | ||||| |||| ||  ||| |||||  ||   |  ||| ||  |||||    ||     ||| ||||  | |      ||||||||||
TGTCAACCATCTGAAAACCCTGCACATAAATGGGGTGGTCTCGGAGAGGTCCTTGGTGGAAATGAGCTGATTGATAGTCAGATCGATATAAAGTTCATAAgtatgcttgccttatcttgacatcctcctgaagtttgttttttcttggactgtgtattgatgcatgtttgtttctgtgactgaattgatttattttgttggcttttcattttattgtttcttttgttttag

upper sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 2
TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttcataccctccttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccctgaccattttacattaaacttctttgttttag
|| |   || |||  || || |||||||||||||||||||| || |||||||| || |||||||| || || ||||| ||  |||| ||||||||  || ||| |  | |            || || ||  |||||| |||   ||    ||||| |         |  |||  ||| |  ||        |||||| | | || || |  |      
TGCCGTTCACCTGGTAATCCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAACTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatggaggtt-----------tctttcatcctattta-tttcataagacccatcagt---------tgacaa--aactggctttaacagttattttataattaatttttaag------

upper sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 2
TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttcataccctccttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccct-gaccattttacattaaacttctttgttttag
|| |  ||| |||  ||  | |||||||||||||||||||| || |||||||| || ||||||||||| || ||||| ||  |||| ||||||||  || ||| |  | |            || || ||  |||||| |||   ||     |||| |  |    |  ||    |||| |||||   |  |  |||||   ||||               
TGCCGTCCACCTGGTAATACTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATTGATAGCCAACTTGAGATAAAGTTCCTAGgtatggaggtt-----------tctttcatcctattta-tttcataagacctatcagtagacaaac--tggctttaacagattttttttaattattttt--ttaag--------------

upper sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 2
TGTCAGCCATC--TGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttt-tcataccctccttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccctgaccattttacattaaacttctttgttttag
   || | |    ||  |   | |||||||||||||||||||| || |||||||| || ||||||||||| |||||||| ||  |||| ||||||||   ||||| |  | | | | |  |||  |     |||| ||  |      |   ||  |  ||      ||  | |  ||||   | ||||                                  
--CCATCTAGTAGTGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAAATTGAAATAAAGTTCCAAAgtatgaaggtttctgttgtactatgt---atttcatagaagagccgtcagttgacaaactggctttaatggatacta-ttgttttcag--------------------------------

upper sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 2
TGTCAGCCATC--TGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatct-tttcataccctcc-ttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccctgaccattttacattaaacttctttgttttag
   || | |    ||  |   | |||||||||||||||||||| || |||||||| || ||||||||||| |||||||| ||  |||| || |||||   ||||| |  | | | |||| |||  |   || | |  |    || |||||  |     |||  |   ||   ||||    |  | ||||                                  
--CCATCTAGTAGTGCTAGTGCTGCACACAAATGGGGTGGTCTTGGTGAGGTCCTGGGTGGCAATGAGCTCATCGATAGCCAACTTGAAATTAAGTTCCAAAgtatgaaggtttctttcgtactatgtatttaatagaagagctgttggatgg-----caaaatggctttaatgcatgctattgttttcag--------------------------------

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|88851745|gb|CI674947.1|CI674947
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATCTGCCCAATTGAACTTGATGACAACAAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|29630127|gb|CB635136.1|CB635136
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCGTTTGCACAATTGAACTTGATGACAACGAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|88591655|gb|CI709704.1|CI709704
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAA
EST: gi|88729589|gb|CI751392.1|CI751392
EST:     CCTTGGCGGCAATGAGCTGATCGACAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTCGCACA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACA
EST: gi|88762940|gb|CI772496.1|CI772496
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAG
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAG
EST: gi|58667768|gb|CK056454.1|CK056454
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|29623264|gb|CB628275.1|CB628275
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|88443541|gb|CI597008.1|CI597008
EST:     C-TTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|88368107|gb|CI574989.1|CI574989
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTC-GGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACCAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|88306502|gb|CI671253.1|CI671253
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAA
EST: gi|29626345|gb|CB631356.1|CB631356
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA
EST: gi|88329904|gb|CI651581.1|CI651581
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGACAAGGGTC
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTC
EST: gi|88391960|gb|CI683780.1|CI683780
EST:     CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAA                         AAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACCAGA
genomic: CCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGA

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: 74 (upstream exon), 73 (downstream exon)
Score: 33

TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgat ... tttgttttagAAAATGTGGAGAAGGGTCCCATTTGCACAATTGAACTTGATGACAACAAGATTCAACAATTTACTGATGCCATTGAAAGGTCATATTGGTTTGAACTCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAGCCATCTGAAAACCCCGCACACAAATGGGGTGGTCTCGGAGAGGTCCTTGGCGGCAATGAGCTGATCGATAGTCAGGTTGATATAAAGTTTTTAAgtaagttgatcttttcataccctccttgattttatttacttttggaatgtgcatcaatgtatgttccttgcaactaaccgatttccctgaccattttacattaaacttctttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT