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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgattgaggaagtccatataccgcatctttttttgacgtgtaaagtgtaatgtttggaatattcaatttatgctgatatacttctaattgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC

Basic information

species Oryza sativa
transcript LOC_Os05g45420.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 10
tttatgattgaggaagtccatat--accgcatctttttttgacgtgtaaagtgtaatgtttggaatattcaattta-----tgctgatatacttctaattgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC
    | | |  | |  | ||||      |  || |||||    |  |||||| ||    |||||| ||  | | ||     | || ||| ||||| | | |||||||||||||||||| |||||||| || |||||||||||| ||||||||||||||||| |||| ||||||||||||||| |||| || ||||||||||||||||
---gtaactt-gtactttcatactggatggttcctttttgttagcataaagtcta---cttggaaaatgtagtctactcaattctaatacacttccactggctgcagCTTTACAAAACGAGGGATGAGAAGTACCTTCTTGACCTGCAAAGGGTCAGTGGATCACATCTTCTCTTTCTGGACTTGTGTTCCGCCTTTCTAACTCAGC
















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|89177900|gb|CI391079.1|CI391079
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|89182012|gb|CI113518.1|CI113518
EST:     AAACTGATGACAGTGAGAAATCGACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|33798304|gb|CF325009.1|CF325009
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|88832439|gb|CI019380.1|CI019380
EST:     TCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: TCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|33798259|gb|CF324986.1|CF324986
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|12405263|gb|AU166864.1|AU166864
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|33797833|gb|CF324776.1|CF324776
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTCTACAAAACAAGGGATGAAAAATACCTTCTTGA
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGA
EST: gi|29680934|gb|CB677209.1|CB677209
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|88437430|gb|CI528789.1|CI528789
EST:     CCACACTGTGAAATTTG-AATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: CCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|86488486|gb|CI131119.1|CI131119
EST:     TGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: TGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|25797845|gb|CA753806.1|CA753806
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|427498|gb|D23565.1|D23565
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAACCAAGGG
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGG
EST: gi|88251491|gb|CI349919.1|CI349919
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|88380597|gb|CI521166.1|CI521166
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGNAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|88968366|gb|CI098608.1|CI098608
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|86494705|gb|CI137338.1|CI137338
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
EST: gi|89177899|gb|CI391078.1|CI391078
EST:     AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAG                         CTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT
genomic: AAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGT

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: 14 (upstream exon), 62 (downstream exon)
Score: 1

GAGTATGATGCATAACAACCATGGCTTTGGTGCAGAATCTGCTATAATTGAAACTGATGACAGTGAGAAATCAACCCACACTGTGAAATTTGAAATTCAGgtatcatttt ... attgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtgtaatgtttggaatattcaatttatgctgatatacttctaattgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC
                                        ttctaat  putative branch site (score: 1)
                aatattcaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgattgaggaagtccatataccgcatctttttttgacgtgtaaagtgtaatgtttggaatattcaatttatgctgatatacttctaattgctgcagCTTTACAAAACAAGGGATGAAAAATACCTTCTTGACTTGCAAAGGGTCAGTGGACCACAGCTTCTCTTTCTGGACCTGTGCTCTGCCTTTCTAACTCAGC

- -atgattg
- - - - - - - - - - - - ccgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat