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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttccattttatcctcacggtgctgtattagaaatttttactgattgtgttgtctacttttctttttctgaacatgcactatatgtttcatctgcttttttctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGGGTTTCAATTCCAAAGGATTATGAAACCGGTGCAAGCAAAGG

Basic information

species Oryza sativa
transcript LOC_Os04g52960.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52960.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G001850_T01 (Zea mays), 3'ss of exon 3
gtaagttccattttatcctcacggtgctgtattagaaatttttactgattgtgttgtctacttttctttttctgaacatgcactatatgtttcatctgcttttttctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGGGTTTCAATTCCAAAGGATTATGAAACCGGTGCAAGCAAAGG
                       ||  | |     |  |||||  || |    ||   |  | ||  | |||||    |  | || || | | ||     |  || ||| | ||||||| |   | |||||||| |||||||| || |||||||| || || ||| |||||||||||||||||||||| || |||| |||||||||
-----------------------gtaatttgagtaaccttttttttggtcacttttcattgtgtttgtgttctgtttct-tatta-atatctgatg---gtacttatttgccagATCCGCACCGCTCTTGAAGAGCATTTTGGATCATGTGGAGATATCACCCGGATTTCAATTCCAAAGGATTATGACACTGGTGTAAGCAAAGG
















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|87035303|gb|CI189925.1|CI189925
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87038432|gb|CI193054.1|CI193054
EST:     TATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: TATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87038991|gb|CI193613.1|CI193613
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87037978|gb|CI192600.1|CI192600
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTGTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|218496529|gb|FG964244.1|FG964244
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87037115|gb|CI191737.1|CI191737
EST:     TATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: TATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|88311073|gb|CI657986.1|CI657986
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTGGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|29667433|gb|CB663708.1|CB663708
EST:     TCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: TCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|218501791|gb|FG963430.1|FG963430
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATATAGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|218494665|gb|FG965505.1|FG965505
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTTTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87041050|gb|CI195672.1|CI195672
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|58687835|gb|CK076522.1|CK076522
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|218499407|gb|FG963731.1|FG963731
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|38481252|gb|CF965341.1|CF965341
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87042161|gb|CI194785.1|CI194785
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|87036541|gb|CI191163.1|CI191163
EST:     GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: GAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
EST: gi|88198885|gb|CI197282.1|CI197282
EST:     TATTAAAGGCTTTGATACTTCTCTTGACATACACCAG                         ATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG
genomic: TATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGG

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: 75 (upstream exon), 48 (downstream exon)
Score: 63

GAGGGACAATAGTTCTTTCAAGAAGCCTGCTCAAAGCTCAGGAAACACTATATTTATTAAAGGCTTTGATACTTCTCTTGACATACACCAGgtaagttcca ... tctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGGGTTTCAATTCCAAAGGATTATGAAACCGGTGCAAGCAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctttttctgaacatgcactatatgtttcatctgcttttttctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGGGTTTCAATTCCAAAGGATTATGAAACCGGTGCAAGCAAAGG
                              tttcatctgctttttt  CT-rich tract
                                        ttttttctttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttccattttatcctcacggtgctgtattagaaatttttactgattgtgttgtctacttttctttttctgaacatgcactatatgtttcatctgcttttttctttactagATCCGGAATTCACTTGAAGAACATTTTGGCTCGTGTGGAGAGATTACACGGGTTTCAATTCCAAAGGATTATGAAACCGGTGCAAGCAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG