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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g47770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
--tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
  ||| |    ||           |||   | ||    |   || | |   |       |||  | || |||     | ||| ||| |||| ||  || ||||||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || || ||| |||| |||||||||||||||
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaag-agctattccagtaactattgattca-ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
--tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG-----------
  ||| |    ||           |||   | ||    |   || | |   |       |||  | || |||     | ||| ||| |||| ||  || ||||||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || || ||| |||| |||||||||||||||           
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaag-agctattccagtaactattgattca-ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 5
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagata-tattgtttactg-ttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
   || |    | |  |    |  |  ||| | |  | |    ||    || ||     |  | | ||  || |   || || ||  | |||||  || |||||||| |||||||||||||||| || |||||||| || |||||| | |||||||| || || || ||| |||| ||||| |||| ||||
--tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagata-tattgtttactg-ttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG-----------
   || |    | |  |    |  |  ||| | |  | |    ||    || ||     |  | | ||  || |   || || ||  | |||||  || |||||||| |||||||||||||||| || |||||||| || |||||| | |||||||| || || || ||| |||| ||||| |||| ||||           
--tgtacgactaatccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G07810.2 (Glycine max), 3'ss of exon 4
tgggttctggaatttttgtccacctaccatctttgtttaa---caattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtc----tgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG--
     |  |  |||||| ||    ||  || |   |  ||     ||| || ||  |   ||      |||     | | ||  ||  |   |||| |    |||||||||||||||||| || ||||| ||||||||||| ||||||||| | || ||||||||  | || ||| | ||||||||| |  |||||  
----gttagccatttttttctttttaa-atttagatgaaagcgtgattgacttggta--ctggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGGT

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 4
tgggttctggaatttttgtccacctaccatctttgtttaa---caattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtc----tgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
     |  |  |||||| ||    ||  || |   |  ||     ||| || ||  |   ||      |||     | | ||  ||  |   |||| |    |||||||||||||||||| || ||||| ||||||||||| ||||||||| | || ||||||||  | || ||| | ||||||||| |  |||||
----gttagccatttttttctttttaa-atttagatgaaagcgtgattgacttggta--ctggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaat-ttgaccgcagatatattgtttactgttgtttcacttgtc----tgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
     |     |||||| ||    ||  || |   |  ||  || |     |   | |||      | |     | | ||  ||| |   |||| |    |||||||||||||||||| || ||||| || |||||||| ||||||||| | || ||||||||  | || ||| | ||||||||| |  |||||
----gttaaccatttttttctttttaa-atttagataaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G36410.1 (Arabidopsis thaliana), 3'ss of exon 4
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
                |    || ||| | |    |    || |     |   | |   |   ||      || | |  |||| |||   || |  |||||| | |||||||| |||||||||||||||||||   | |||||  | ||| |||| ||  | || ||| | || |||||| | |  |||
---------------gtaagtacatacaaacacaatgactcactctgtttcaaagtccaatgacaagacccttctatg-tgttcttttgattat--gcagATGTCTTGTATGATTCGTGGTCACCGGCGATGAGACTAAGTTCCATCTGTCTCAGCATTCTCTCAATGCTCTCCAGCTCATCCGTGAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
tgggttctggaatttttgtccacctac-catctttgtttaacaatta-acatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
    |  | ||||      |   | || ||    ||    | | |    || || |||   |       | |    | |    ||  ||    |     ||||||||||||||||||| |||||||| || ||||| || || ||  | || ||||| ||| | || ||||| || || ||| |||  |||
--aatcatagaatgaagaacactcgacgcagtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

upper sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
-tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtca-atttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
  | ||||   | ||   |   ||   |  | | |  || | | |||||||||    ||| |       ||  || |  |   |||  |  | | ||  |||||||  | |||||||| |||||||| || |||||||| |||||| | || ||||| ||| ||||||||||||| || ||| | |  |||
acgagttcccaacttaacgaaaactatctctgtgtacttga-atttaacatgttgcgtttaattaagactaatttctgcaaacttggctt-cgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

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|88996042|gb|CI037333.1|CI037333
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|88205530|gb|CI205379.1|CI205379
EST:     ATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: ATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|8859712|gb|AU097030.1|AU097030
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|89177790|gb|CI390969.1|CI390969
EST:     CATTTACAGCAATGGGCATATCTGTTAAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: CATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|33813694|gb|CF332734.1|CF332734
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|87034301|gb|CI188925.1|CI188925
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|86432724|gb|CI086335.1|CI086335
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTNAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|88206195|gb|CI206044.1|CI206044
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|88429510|gb|CI551575.1|CI551575
EST:     TTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
EST: gi|11565148|gb|AU165784.1|AU165784
EST:     TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAG                         ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA
genomic: TCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTA

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: 50 (upstream exon), 73 (downstream exon)
Score: 22

GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgat ... ttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG
                                       tttcactt  CT-rich tract
                   agatatattgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- ggttctg
- - - - - - - - - - cacctac
- - - - - - - - - - - - - - - - - - - - - - -aacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttactg