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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctctttcatttattttgctccttacatcttgttagtttgtatattaaaaaaaagctatgatttttggtcacag

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08560.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 6
ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctctttcatttat---------tttgctccttacatcttgttagtttgta-tatt----aaaaaaaagctat--gatttttggtcacag----------------------------------------------------------------------------------------
 || | |||||| ||||| || || || |||||| | || || || ||||| ||||| || ||||| || ||| |||| |||||||||||||| ||||||||| |    |||  || ||          | |||||         || |   |||| ||||    ||  |||||  |   || |     |  | |                                                                                        
TTTTACTGCTAAACTTCAGGAAGTGGAAGATTGGCTTTATGATGAGGGTGAAGATGAAACTAAAGGTGTATATATTGCCAAGCTTGAAGAACTCAAAAAGgttaggaagttttgttgataagggaatcctagctcccattcctcagtcaaactgtaatattgtgcaaggaaaagggaccagagtacctcttgctgttatcctttgtgtttttttgcacaaacataaatggtgtgaggtatttccatgctagttttaacataggcaatctcaatgtgattgcag

upper sequence: LOC_Os01g08560.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 7
ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtt---tgtctctttcat------ttattttgctcctta------catcttgttagtttgtatattaaaaaaaagctatgatttttggtc-acag
|||| | || || || || || ||||||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||| || || || || |||||      |   | | ||      |||| |||  |   |      ||| ||    | |  | | |||| | |    |  ||||  |  |   |||
ATTCCTGGCGAATCTGCAGGAAGTTGAGGATTGGTTGTATGAAGATGGGGAAGATGAGACCAAAGGTGTTTATGTTGCGAAGCTCGAGGAGCTCAAGAAGgtaatgcatgcatatgatgacactttatattgtgcaggaagaaatcatatttcaggataatgttttaacagaggagtgggattaatattttgcag

upper sequence: LOC_Os01g08560.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 7
ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctctttcat---------ttattttgctcctta------catcttgttagtttgtatattaaaaaaaagctatgatttttggt-cacag
|||| | || || || || || ||||||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||| || || || || |||||    |      ||         |||| |||  |   |      ||| ||    | |  | | |||| | |    |  ||||  |  |   |||
ATTCCTGGCGAATCTGCAGGAAGTTGAGGATTGGTTGTATGAAGATGGGGAAGATGAGACCAAAGGTGTTTATGTTGCAAAGCTCGAGGAGCTCAAGAAGgtaaaccatgcatatgatgacactttatattgtgcaggaagaaatcatatttcaggataatgttttaacagaggagtgggattaatattatgcag

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|58677519|gb|CK066206.1|CK066206
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|218481790|gb|FG945721.1|FG945721
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATAGAGGCAAGGTACAAGGAATGGATGGACAGAGGCC
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCC
EST: gi|27921378|gb|CB097186.1|CB097186
EST:     GAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: GAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|58683636|gb|CK072323.1|CK072323
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|29678339|gb|CB674614.1|CB674614
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|218478821|gb|FG953668.1|FG953668
EST:     AGGATGAGACCACAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|58597595|gb|CK008123.1|CK008123
EST:     AGGATGAGACCCAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTACAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|87021150|gb|CI271957.1|CI271957
EST:     AACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|2310021|gb|C26176.1|C26176
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTNGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|29636673|gb|CB641682.1|CB641682
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|27553959|gb|CA997859.1|CA997859
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
EST: gi|86829544|gb|CI286738.1|CI286738
EST:     AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAG                         GTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT
genomic: AGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCT

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: 73 (upstream exon), 71 (downstream exon)
Score: 120

ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctct ... ttggtcacagGTGGGGGGTCCCATTGAGGCAAGGTACAAGGAATGGATGGACAGAGGCCCTTCCATCGACCAACTTGCTTACTGTATCAACAGTTTCAGAGATGCTGCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATTGCTAAGCTTCAAGAGGTTGAGGATTGGTTGTACGAAGATGGTGAGGATGAGACCAAAGGAGTGTATGTTGCTAAGCTTGAAGAACTTAAAAAGgtttgtctctttcatttattttgctccttacatcttgttagtttgtatattaaaaaaaagctatgatttttggtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC