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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacagcaccaattgtctgccccttctagatttcctttttggccattataatcatctctttttgttattttcagtacatatccccattagtagctgtttgtgtgtttgactgctgtgttctttaagtccataaatcttaattgtttactattagttacctttgagaactcacatggctatttgatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCCAGGTTGTTCAATGCATCTGTCCATTCAGAATTTGAAGATGCGCTTGAAT

Basic information

species Oryza sativa
transcript LOC_Os06g47350.2
intron # 14
splice site 3'
intron type U2

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|27334393|gb|CA882844.1|CA882844
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|2799623|gb|AA752612.1|AA752612
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|58668152|gb|CK056838.1|CK056838
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|218504600|gb|FG967431.1|FG967431
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|66922574|gb|CX109422.1|CX109422
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|218500322|gb|FG953822.1|FG953822
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|218504331|gb|FG952706.1|FG952706
EST:     GGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: GGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|218499202|gb|FG956934.1|FG956934
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|58668829|gb|CK057515.1|CK057515
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|58680790|gb|CK069477.1|CK069477
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|56158395|gb|AU075492.2|AU075492
EST:     TTAACATGCCATTTGGATATATC-TGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
EST: gi|218492292|gb|FG954140.1|FG954140
EST:     TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAG                         GTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC
genomic: TTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCC

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: 73 (upstream exon), 74 (downstream exon)
Score: 95

CTTTCGCTTAAGATCTATTATGGACTACCCAAATCTTAAGGCACAGCTTTTTAACATGCCATTTGGATATATCTTGACACACCCACTGGAACCTTTAAAGgtttgtacag ... gatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCCAGGTTGTTCAATGCATCTGTCCATTCAGAATTTGAAGATGCGCTTGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgtttactattagttacctttgagaactcacatggctatttgatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCCAGGTTGTTCAATGCATCTGTCCATTCAGAATTTGAAGATGCGCTTGAAT
                                        tatttgatatttta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacagcaccaattgtctgccccttctagatttcctttttggccattataatcatctctttttgttattttcagtacatatccccattagtagctgtttgtgtgtttgactgctgtgttctttaagtccataaatcttaattgtttactattagttacctttgagaactcacatggctatttgatattttagGTTTGCTTGCCATCGATAGTTGATGAGTTCCTGAGGCAGGCCAAGGCTGCCAGGTTGTTCAATGCATCTGTCCATTCAGAATTTGAAGATGCGCTTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG