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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgataatgatgcgcttcccaaataacacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 16
gtatgcttgataatgatgcgcttccca--aataacacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG
                | ||||| |    |   |  ||| || | | ||    |||||   |||||||||||||   ||||    |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||||
---------------gtacgcttgcttttacgcatgcaattgctagaaacgctttgcattgttttcactgactt---tgtgccttcagAATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G126453_T01 (Zea mays), 3'ss of exon 20
gtatgcttgataatgatgcgcttcccaaataacacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG
||| | ||| |  | | |||   |    |||  |           ||     ||||   ||||||| | |||  |||   || |||||||| || |||||||| || ||||||||||| |||||||| || |||||||||||||||
gtacgtttgctctt-acgcgtgccattgatagaa----------aaaccctctgcatggttttcaccggcttcgttg--ctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG
















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|55409323|gb|CV721699.1|CV721699
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|58653111|gb|CK041791.1|CK041791
EST:     TATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|58691499|gb|CK080186.1|CK080186
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|29614541|gb|CB619554.1|CB619554
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|8860068|gb|AU097386.1|AU097386
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|218497816|gb|FG965087.1|FG965087
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|11171080|gb|AU163614.1|AU163614
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|29682150|gb|CB678425.1|CB678425
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATTTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|15857794|gb|BI810606.1|BI810606
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACC-CAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|8860101|gb|AU097419.1|AU097419
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAA-TGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|86479265|gb|CI121898.1|CI121898
EST:     TATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCGTGAGAAG
genomic: TATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|86849466|gb|CI299672.1|CI299672
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|27554453|gb|CA998353.1|CA998353
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
EST: gi|58686681|gb|CK075368.1|CK075368
EST:     TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAG                         AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG
genomic: TGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAG

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), 74 (downstream exon)
Score: 16

GATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttga ... gtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG
                                cactgac  putative branch site (score: 16)
                                              tgttccc  putative PPT
                        acaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgataatgatgcgcttcccaaataacacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccagAATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG