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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcatatctgtcatgttccacctccacacaaccaaaacttatttcaaactgaattctctgtaatatactatgcctgtatgattcatcag

Basic information

species Oryza sativa
transcript LOC_Os01g73500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73500.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G167758_T01 (Zea mays), 5'ss of exon 3
GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaac----atcatatctgtcatgttccacctcca----cacaaccaaaacttatttcaaactgaattctctgtaatat--actatgcctgtat---gattcatcag---
|||||||||||||||||| || |||||||| || || ||||||||    |  |   ||   || |   ||  | |    ||   |||   |    |  |   ||  |  |||||  | |  || |||| || ||   |||     ||   
GGTTAAGCAGATCAAATCAGCGTTCTACACGCTGCCAAAGgtaacggctactactcctaatatatataacaacgatatccatggccatggccatatcgatggtggttcttctgttctctgaaccatgcatgcatatggatgtgctagcag
















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|88571055|gb|CI662428.1|CI662428
EST:     GGTTAAGCAGATCANATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTA
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTA
EST: gi|33662848|gb|CF293815.1|CF293815
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|33683454|gb|CF311693.1|CF311693
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|33659979|gb|CF290946.1|CF290946
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|55430712|gb|CV728357.1|CV728357
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|88344530|gb|CI637215.1|CI637215
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|25803799|gb|CA759760.1|CA759760
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|33665646|gb|CF296613.1|CF296613
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|38475002|gb|CF959135.1|CF959135
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTA
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTA
EST: gi|88340926|gb|CI637086.1|CI637086
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|33659959|gb|CF290926.1|CF290926
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|88290458|gb|CI665247.1|CI665247
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|33659939|gb|CF290906.1|CF290906
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|66916268|gb|CX103116.1|CX103116
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|88327415|gb|CI645201.1|CI645201
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|2428527|gb|C72990.1|C72990
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACC
EST: gi|88689446|gb|CI733022.1|CI733022
EST:     GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAG                         TTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAA
genomic: GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAA

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: 40 (upstream exon), 68 (downstream exon)
Score: 15

GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcat ... gattcatcagTTATTCGGTGAATCCAAAATCGTGGAGTACACAATTACAGAAAACGAAACCGCGCCCGGAAAAGTCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTAAGCAGATCAAATCGGCCTTCTACACACTCCCCAAGgtaacatcatatctgtcatgttccacctccacacaaccaaaacttatttcaaactgaattctctgtaatatactatgcctgtatgattcatcag

- - - GCAGAT
- - - - AGATCA