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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgagcattcctaagtgttgaatctaccatcttctatactggaagatttttgttttccttcaaaagctaaccccacaccacacacaccccacccc...

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 14
ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatga-gcatt----cctaagtgttgaatctaccatcttctatactg--gaagatttttgttttcct---tcaaaagctaaccccacaccacacacaccccacccc
|||||||| || || || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||| ||||||| ||||  ||||    ||    | || | |||    | ||| | |  |  | |||  |  || |   |   | || ||  ||      |  | | | |         
ATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAGgtaacatgacacattagttccctgatatt-attctttttttttcgaaaacgcaggagagctgcgtatcattatattaagaggaaaaaggtgaggatagaaa---------

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G312026_T01 (Zea mays), 5'ss of exon 14
ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgagcattcctaagtgttgaatctaccatcttctatactggaagatttttgttttccttcaaaagctaaccccacaccacacacaccccacccc------
|||||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||||| ||| |||    |      |||   ||   |  |   | |      ||    |  || |  |  || || |       | |  ||                 
ATTGTTGCCTTTCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATACAGCAAATTCATTGTTCAGgtaacatg-gcacatttgttccctgatattattcttattcttgcc-----atcccagggtttcagcggaaactcattatgttcaaatcattttaaggatgtggagt

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 5'ss of exon 14
ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatga-gcattcctaagtgttgaatctaccatcttctatactggaagatttttgttttccttcaaaagc-taaccccacaccacac-acaccccacccc
||||| |||||||| || || ||| | ||||||||||||||| | ||||| ||||||||||| |||||||| || || | ||| ||||||||||| ||||||  || |   || | | | | ||  || |   ||  |  |  |||  |  ||||   | |  |||     | | |  ||  | ||           |  | 
ATTGTGGCTTTTCTCATCCCCCTTTTAGACGATAAATTTCCTTTGATACGAAGTATTACTTGCTGGACCCTTTCTCGGTTTAGCAAATTCATTGTTCAGgtacaattataaatacattattcttccattt--tatagttgaagctgtgaacttttccatgtatttcttgttcatgaatccttaacatgttgtgtttgaggc-

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|33797567|gb|CF324643.1|CF324643
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTC
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTC
EST: gi|33678128|gb|CF306367.1|CF306367
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58668781|gb|CK057467.1|CK057467
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58612862|gb|CK040574.1|CK040574
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATTCCAATGGTCGTGAACAATTTGATAAAATCCTC
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTC
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTACAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
EST: gi|58608786|gb|CK036819.1|CK036819
EST:     GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG                         AGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT
genomic: GGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGT

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), 46 (downstream exon)
Score: 25

ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgag ... gctgatgcagAGCCTAGAGCATCCCAATGGTCGTGAACAATTTGATAAAATCCTCTTAGGTTTATTAAGGAGGGTTTTGGATACTAACAAAAGAGTGCAGGAGGCGGCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAGgtaatatgagcattcctaagtgttgaatctaccatcttctatactggaagatttttgttttccttcaaaagctaaccccacaccacacacaccccacccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccacc