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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagatcactgtaaaacttgcttgttgtggtgatacttttggatgtgtctatgtgaatttcagttttttctacagttatggtttgagcacaacgaaaaacttaatacaataacattatacctattggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA

Basic information

species Oryza sativa
transcript LOC_Os02g35470.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 4
gtacaagatcactgtaaaacttgcttgttgtggtgatacttttg-gatgt---gtctatg----tgaatttcagtttt----ttctacagttatggtttgagcacaacgaaaaa-cttaatacaataacattatacctattggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA
    || |  |      ||||||||  |  |||| |  |||  | |||||   ||||  |    |||  || | | ||    || |  | ||||| | | | ||||   ||    ||| ||| |  ||  | ||| | || | |||||| ||||| || |||||||||||||| |||||||| ||||||||||||||  | || | || |   ||  |||| ||| | || |||||||||||||| |||
--gtaaaaaaatc----aacttgctcctcatggtaacgcttgggagatgttctgtcttggaaattgagatttactgttgctattgtgaatttatgatattatcacattaaaggctcttgatatacaaaactaatatccat-gaaaacagATCCTCCCCCAAAAGAATTGAAGGGCCTGATGGAAGAAATCTTCAGCTCCAGTTCAGAAGTCAGTTGGCTCTTCCAATCTTCACTGGTGGAAAAGTTGAA

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 4
gtacaagatcactgtaaaacttgcttgttgtggtgatacttttg-gatgtgtctatgt--gaatttcagttttttc--tacagttatggtttgagcacaacgaaaaacttaatacaat---aacattatacctat-----tggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA
||| || |  |      ||||| |   |  || |||  |||  | ||||| ||| | |  ||| || || ||| |   |    || || | | | ||||   ||     |     | |    | || | ||  ||     || |||||| ||||| || |||||||||||||| |||||||| ||||||||||||||  | || | || |   ||  |||| ||| | || |||||||||||||| |||
gtaaaaaaaaatc----aacttacacttcatgttgacgcttgggagatgt-tctgtcttggaaattgagatttattgttgatattgtgatattaccacattaaaggctcttgggaagttgggatatgaaactaatatatatgaaaacagATCCTCCCCTAAAAGAATTGAAGGCCCTGATGGAAGAAATCTTCAGCTCCAGTTCAGAAGTCAGTTGGCTCTTCCAATCTTCACTGGTGGAAAAGTTGAA
















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|29662458|gb|CB658733.1|CB658733
EST:     TGGGTCCTGCCATAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: TGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|58695876|gb|CK084563.1|CK084563
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29675099|gb|CB671374.1|CB671374
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29674900|gb|CB671175.1|CB671175
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29677880|gb|CB674155.1|CB674155
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|58677698|gb|CK066385.1|CK066385
EST:     GCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGNCTTA
genomic: GCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAG-CTTA
EST: gi|29630082|gb|CB635091.1|CB635091
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|58686392|gb|CK075079.1|CK075079
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29635770|gb|CB640779.1|CB640779
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29626070|gb|CB631081.1|CB631081
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
EST: gi|29629686|gb|CB634695.1|CB634695
EST:     GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAG                         GTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA
genomic: GAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAA

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: 56 (upstream exon), 65 (downstream exon)
Score: 28

GTAAGCGAAGAGGTAGAGCGTGCTTTAGCCAAGTTGGGTCCTGCCAGAATTCAGGGAAGgtacaagatc ... ttggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgagcacaacgaaaaacttaatacaataacattatacctattggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA
                            caataac  putative branch site (score: 28)
                aaaaacttaatacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagatcactgtaaaacttgcttgttgtggtgatacttttggatgtgtctatgtgaatttcagttttttctacagttatggtttgagcacaacgaaaaacttaatacaataacattatacctattggaaacagGTCCTCTCCAAAAAGAATTGAAGGACCTGATGGGAGAAATCTTCAGCTTAAATTTACAACTAGATTATCTCTACCACTGTTTACTGGTGGAAAAGTAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA