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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTTTCGACTTTCTCCTCTTAAAGGGTGTCCCACGTACCCCGACGAGCAATTG

Basic information

species Oryza sativa
transcript LOC_Os05g06430.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 10
gtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTTTCGACTTTCTCCTCTTAAAGG--GTGTCCCACGTACCCCGACGAGCAATTG
||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || ||||||||  || ||  |||   |||| ||||||||||||||||| ||||||||| || | ||||||||||| |||||||  ||||| || | ||||   ||  ||||   || || |  || | | 
gtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaatttccatattttattgtattgtagTCAATCAGTCCTTCCAAAGCTGATGAATTCATCGTTAAGAAGAACATTCTTTCGATATTCTCTTCGTGAAGGTGATGATCCACA-GCCACGGCCTGCCAGT-
















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|5003011|gb|AU068120.1|AU068120
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     CTGAATACACTAAGAAGGAATCTGAGAAGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTC
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTC
EST: gi|2799505|gb|AA752494.1|AA752494
EST:     CTAAGAAGGAATCTGAGAGGCTTCAACGCATGTNGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|3768455|gb|AU032482.1|AU032482
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|58672427|gb|CK061113.1|CK061113
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|86513133|gb|CI155766.1|CI155766
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|88248551|gb|CI248400.1|CI248400
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|163925853|gb|EG714953.1|EG714953
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|11026410|gb|AU163011.1|AU163011
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT

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), 74 (downstream exon)
Score: 25

GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTTTCGACTTTCTCCTCTTAAAGGGTGTCCCACGTACCCCGACGAGCAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTTTCGACTTTCTCCTCTTAAAGGGTGTCCCACGTACCCCGACGAGCAATTG
                         atctgat  putative branch site (score: 25)
                                       cttcatc  putative PPT
     atcatattacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTTTCGACTTTCTCCTCTTAAAGGGTGTCCCACGTACCCCGACGAGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC