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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG

Basic information

species Oryza sativa
transcript LOC_Os07g08760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124965_T02 (Zea mays), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgtt-tgat---gtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctt-tgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
   ||      || || | |||||  ||  |||     ||   ||  |  || |||| |  |  | ||  | |||| | || | | || ||   | |  || |||| ||||||||| |||||||| || ||||||||||||||||||||||| ||||| || |||||||||||||||||||||| ||| |||||||| |||||||
---tcagaagattgcagttaatctgtgtaatgactaaatggtaaatgctttaccata-atttcttcgtata-catcaactgaatttattttaaatgtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 3
---atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctt-tgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
   | ||      ||       |||||  ||      |||| ||||   |  |  |||   |||      |||| |  ||   | || ||   |    || | ||| ||||||||| |||||||| || ||||||||||||||||||||||||||||| || |||||||||||||||||||||| ||| |||||||| |||||||
aacagttagaagattgcagtaaaatctgtgtc----atgactaaatgttttac-cataatatatttgtatacatatcctgagtttattttaaatacatttattagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACTCCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgt-ttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
|    || | ||    || | |  |  | ||  | |    |  || |    | ||  |  |||   || ||||| |||    ||  |   | || |   ||   || ||||   | ||| ||||| | ||| | ||||| ||||| ||||| ||| | || || |||||||||||||||||||| |||||||  || ||||
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgt-tggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G23080.2 (Arabidopsis thaliana), 3'ss of exon 3
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
                 | |||||| |||| |      | ||         |||| |   |||| |     || |  |   |   ||   ||| |||| || | || ||| |  | ||  ||||||| ||| ||||||||||||  || || ||  ||||||| |||||||||||||| ||||| ||||| |  || ||||
----------------gtaaatctaagttttaaagactctaact------ttatatgacttagttc-----ctgaaaggtgg---ttatgttggttgtcagATAGGTCCTGTTGTTTATCGTAGTCGAACTGTTTTTGAGGATGTAACACCAGACATTGTTAGGGATTTCTTCTGGGACGATGAGTTTCGACCTAAATGGG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacat-ctaatggactgatc--ttcctttgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
   |  | |   |  ||||||     |  |  | | |   | |  ||   | | |  ||  |    |   |  |  | | |||||   |    ||| || | ||   || ||| | || ||  | || || ||| | ||||||||||| ||||| ||  ||||||| |||||||||||||||||||| ||||| |  || ||||
--gtgttcttgctataatgaaatggggaat--tcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
-------atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
         |   ||| | |  | ||    ||  ||| |  |  |    |  |  | | |||   |  | |  |  | |  ||    || | || ||||      ||   || || |   ||||  ||||  | ||| | ||||||||||| ||||| ||| | |||||||||||||||||||||||||| ||| | |  || ||||
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcatt--agtaaccgataa--tggtgtttctttatc---agAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG

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|29659937|gb|CB656212.1|CB656212
EST:     AACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAG                         GTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: AACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
EST: gi|30226837|gb|CB964729.1|CB964729
EST:     CTGGCGCCGTGAGCCTGAG                         GTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: CTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
EST: gi|14981939|gb|BI306617.1|BI306617
EST:     CAAGTGCCCGGCGCCCGTGAGCCCTGAG                         GTGGGACCTATCACTGTACTGTAGTCGCACCATTTTTGAGGATGCTACTC
genomic: CAAG-GCCTGGCG-CCGTGAG-CCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCA-TGTACTGTAGTCGCACTATTTTTGAGGATGCTACTC
EST: gi|29659876|gb|CB656151.1|CB656151
EST:     AACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAG                         GTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: AACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
EST: gi|30228065|gb|CB965957.1|CB965957
EST:     CTGGCGCCGTGAGCCTGAG                         GTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: CTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
EST: gi|23512848|gb|BU672864.1|BU672864
EST:     GCCGTGAGCCTGAG                         GTGGGA-CTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: GCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
EST: gi|30228719|gb|CB966609.1|CB966609
EST:     CTGGCGCCG-GAGCCTGAG                         GTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT
genomic: CTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCT

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: 71 (upstream exon), 69 (downstream exon)
Score: 59

ACTTCTTGATAACAAGGAGAGTGGGGATACAACATGGCAGCATTTGATGGAACGTACCACTTCCAACATGACTTACAAGGCCTGGCGCCGTGAGCCTGAGgtatgttttc ... ttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
                                gactgat  putative branch site (score: 59)
                                      tcttcctttgcttgt  CT-rich tract
            ttatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - cctgtct
- - - - - - - - - - - - - - ttgatgt
- - - - - - - - - - - - - - - - - -gaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcaac