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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagccttacgtcagatgaataatttaatattccctccatctacttttgatagtcatatttcatcttggcacaatgaccaaggataagtaattctac...

Basic information

species Oryza sativa
transcript LOC_Os05g44360.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G060611_T02 (Zea mays), 5'ss of exon 3
TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcc-ttacgtcagatgaataatttaatattccctccatctacttttgatagtcatatttcatcttggcacaatgaccaaggataagtaattctac--------
||| |||| |||||||| || || ||||||||||||||||||||||| ||||||||||||| ||   | |     || ||  ||||| |||| |  | || |   | ||  ||  ||   | | || |||  | |         |   |  | || |        
TTTCTGTCCAAGAATGGAATTTATGAGTTCTGGAACTGGTTTGATGATAGGACATGgtaagggcagctccaaactatcaaccatttagtattgcg-caatttctgtgtggaaggaatcaatta-ctcggctgatttcgttgctgttgctgctgctgctgctttag

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G08410.1 (Glycine max), 5'ss of exon 3
TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagccttacgtcaga--tgaataatttaatattccctccatctac--ttttgatag-----tcatatttcatcttggcacaatgaccaaggataagtaattctac-
|||||| | ||||||||||| || || ||||||||||||||||||||  | || |||||||    |   ||      ||||  | ||  |  ||  | | |  |   |||  | ||     |  || |   ||| |  | |||| |            |||  |  
TTTTTGACAAAGAATGGGATATATGATTTCTGGAACTGGTTTGATGATCGAACTTGgtaagttgatggtgtttatattgaaacactttttcctctatacttgcatagtttaaacaggttgttgttaatgtttctggatataatgtctgttacctttccatttcaag

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G01270.1 (Glycine max), 5'ss of exon 3
TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagccttacgtcagatgaataatttaatattccctccatctacttttgatagtcatatttcatcttggcacaatgaccaaggata-agtaattctac-----------------
|||||| | ||||||||||| ||||| ||||||||||||||||||||  | || |||||||    |   ||      | | |  || | || ||||  | |||||  | ||||   |     |  | |   ||||     ||||| | |     |                   
TTTTTGACAAAGAATGGGATATACGATTTCTGGAACTGGTTTGATGATCGAACTTGgtaagttgatggtgtttat--attgaaatagtttttcctc--tttacttgcg-tagtttaaacaggttgttgttaaatgtttctggatataatgtccgtgttacctttccatttcaag

upper sequence: LOC_Os05g44360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagccttacgtcagatgaat-aatttaatattccctccatctacttttgatagtcatatttcatcttggcacaatgaccaaggataagtaattctac
|| || ||||||||||| || |||||||||||||| ||||||||||| ||||| ||||||          |||||    |   | || || |  || ||    | ||  |    | |||||  | |   |    | |      || ||         
TTCTTATCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTGgtaat--ttgaggatcagaaattttggtctattactgtcttcaatagcattgta----cttattttgtttcccccattttatttgatattag---------

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|88395376|gb|CI611293.1|CI611293
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88388047|gb|CI590323.1|CI590323
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCC-GTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
EST: gi|88391883|gb|CI603402.1|CI603402
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGAGAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88689170|gb|CI732746.1|CI732746
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
EST: gi|29630981|gb|CB635990.1|CB635990
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88386226|gb|CI572843.1|CI572843
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88728375|gb|CI751885.1|CI751885
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTA
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTA
EST: gi|88412871|gb|CI576135.1|CI576135
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|25797492|gb|CA753453.1|CA753453
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88693052|gb|CI736627.1|CI736627
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACAT
EST: gi|88422398|gb|CI689215.1|CI689215
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGCGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88431648|gb|CI576839.1|CI576839
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88420887|gb|CI620205.1|CI620205
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTT-GATGACAGGACATG                         GTATCCCCT-GGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88406275|gb|CI596402.1|CI596402
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|29643810|gb|CB648817.1|CB648817
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88691581|gb|CI733659.1|CI733659
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCCTGGCCGTGTGATTGGC
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGC
EST: gi|88406160|gb|CI593940.1|CI593940
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACA
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACA
EST: gi|88305575|gb|CI631942.1|CI631942
EST:     TCGAAGAATGGGATCTACGAGTCCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88390581|gb|CI609206.1|CI609206
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
EST: gi|88345883|gb|CI632356.1|CI632356
EST:     TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATG                         GTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT
genomic: TCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATT

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), 64 (downstream exon)
Score: 10

TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagcct ... tctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATTGACAGCTGGAACCATTTGGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTGTCGAAGAATGGGATCTACGAGTTCTGGAACTGGTTTGATGACAGGACATGgtaagagccttacgtcagatgaataatttaatattccctccatctacttttgatagtcatatttcatcttggcacaatgaccaaggataagtaattctac

- - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctcc