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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtcgttgcactatttgagccaacaccattttttagagaaagttttagttcttggcatcactattgtgttacatttttctaattacttcatcatacaaacatgcactgccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC

Basic information

species Oryza sativa
transcript LOC_Os05g04340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 10
gtgagtgttgtcgttgcactatttgagccaacaccattttttagagaaagttttagttcttggcatcactattgtg--ttacatttttctaattacttcatcatacaaacatgcactgccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC
                                                |||| |  ||| || |   | | || |   | | ||| || |||||| |||   ||  |||  |  | |                  || ||   |||||   || ||     ||| ||  |||  ||| || |||   || || ||||| |||||||| ||||||||||| || ||| |||| || || |||| |||||| || ||||| |||||||   || 
------------------------------------------------agttctctttcctgactgaatttttataaataatattgttataattatttc-caattgaaaattatatta-----------------agctat--attgtttgttcctgg---tgctat-gcagCTGGAGGCCTTGGCTCACCCATTCTTTGATGAACTGCGTGATCCAAATACTCGCCTACCAAATGGGCGTTACCTTCCCCCACTCTTTAACTTCAGAGCCA

upper sequence: LOC_Os05g04340.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G01280.2 (Glycine max), 3'ss of exon 11
gtgagtgttgtcgttgcactatttgagccaacaccattttttagagaaagttttagttcttggcatcactattgtg-ttacatttttctaattacttcatcatacaaacatgcactgccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC
                                                               | || || |  ||  |  |||||| ||| || |   |  || ||  ||   |    |||  || ||     || ||   |||||   || |||    ||| ||  |||  ||| || ||| | ||||| ||||| |||||||| ||||||||||| |||||| |||| || || |||| |||||| || ||||| |||||||   || 
--------------------------------------------------------------tcttctctttcctgactgaatttttataactaatat-ttttataattatttccca--ttgaaaattatattaagctat--attgtttgttccttg---tgctat-gcagCTGGAGGCCTTGGTTCATCCATTCTTTGATGAACTGCGTGATCCAAATACCCGCCTACCAAATGGGCGTTACCTTCCCCCACTCTTTAACTTCAGAGCCA

upper sequence: LOC_Os05g04340.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 11
gtgagtgttgtcgttgcactatttgagccaacaccattttttagagaaagttttagttcttggcatcactattgtgttacatttttctaattacttcatcatacaaacatgcactgccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC
                                                                     |||  ||| |  |  |   |   |  | |  | |     || ||    |||       ||| | | ||   || |     ||| ||||||| | ||  |||  ||| || |||||||||||||| || ||||| || ||||| |||||||||||  | || || || ||||||||||| ||  | |||||||||||||| |
-------------------------------------------------------------------tatatgctgtgat-tcctggaaggcatgtgaagacagttggatccaacctcttctttcaaacttg-aatttttgacttgatgtttatttattttctat-gcagCTGGAGGCTTTGATCCATCCCTTTTTTGATGAGCTACGTGAGCCAAACACCCGTCTGCCAAATGGACGTTTCCTTCCCCCATTGTTCAACTTCAAGCCTC

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|29629993|gb|CB635002.1|CB635002
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|29629559|gb|CB634568.1|CB634568
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|25804076|gb|CA760037.1|CA760037
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TNGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|86251622|gb|CI016911.1|CI016911
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|51946083|gb|CV152424.1|CV152424
EST:     NTCTCGTCTNCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|29623769|gb|CB628780.1|CB628780
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|58612435|gb|CK040147.1|CK040147
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGT
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGT
EST: gi|88839091|gb|CI378015.1|CI378015
EST:     TCTCCAGGC-TTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: TCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|87024245|gb|CI256986.1|CI256986
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|86433457|gb|CI093800.1|CI093800
EST:     GGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: GGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
EST: gi|88828410|gb|CI073280.1|CI073280
EST:     ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCT                         TCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC
genomic: ATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACC

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), 54 (downstream exon)
Score: 34

ATCTTCCATAAAAGAATGCCTGCTGAAGCAGTCGATCTCGTCTCCAGGCTTTTGCAGTATTCACCATACCTCCGGTCCACTGCTgtgagtgttg ... gccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC
                                  tttctttatttgcc  CT-rich tract
                                 atttctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttgtcgttgcactatttgagccaacaccattttttagagaaagttttagttcttggcatcactattgtgttacatttttctaattacttcatcatacaaacatgcactgccttgccaagtactagtagttacagattgtgcatttctttatttgccattacagTCGGAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCC

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