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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctccttagctttctggtttccttgtctttacctttgggataaaaacggc...

Basic information

species Oryza sativa
transcript LOC_Os08g06110.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G014902_T01 (Zea mays), 5'ss of exon 8
AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctccttagctttctggtttccttgtctttacctttgg-gataaaaacggc-
|||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| |||||| || |||||||| |||||| ||||  || || ||||||| |||||| |  || |||| |||| ||| | ||||||| |  ||||  |||||        
AGCATGTTGGGACAAAGACAGCCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAGgttgtttctctatctgattggctagtg--cccttgtttggttcagcgctgttaccctagcattctagttgcattgtcttcatatttgctgataacgtgaatg

upper sequence: LOC_Os08g06110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G45030.1 (Glycine max), 5'ss of exon 3
AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctcctt-agctttctggtttccttgtctttacctttgggataaaaacggc
||||| | || |||||||| |||||||| ||||| ||||||||||| || ||||| || |||||   |||  || ||| |   |  |   |  |  ||    |||   |   | |  || |  ||| || ||    |   ||| |   ||   ||  |||   
AGCATATAGGAACAAAGACTGCTGTGCAAATCAGGAGTCATGCTCAGAAATTCTTTACAAAGgtaaatcca-taccttctcacctgggattattcattgaaatttttggtcctataattcaaatttatgcttcatcttgatttgctgctgatttattaaccaa

upper sequence: LOC_Os08g06110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G01060.2 (Arabidopsis thaliana), 5'ss of exon 4
AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctcct-tagctttctggtttccttgtctttacctttg-----ggataaaaacggc
| ||| ||||||||||||| ||||| ||||||||||||||||| |||||||||||||| |||||   |     ||| | |  |       || ||||       |  || |||||  | ||    |    |||  |  | |  | || ||     |  || ||   ||
AACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAGgtaagttgatgatcctttcaga------tctttttaaaacactttcgttatcttgtgtaaaggtaccattttttcatatcgatctatgactatgtttagaagttgc

upper sequence: LOC_Os08g06110.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0048g02410.t01 (Vitis vinifera), 5'ss of exon 3
AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctcct-tagctttctggtttccttgtctttacctttgggataaaaacggc
| ||| | || |||||||| |||||||| |||||||||||||| ||||| |||||   ||| | ||   |  || ||| |       ||||  || | |   | || |  | | || | | ||||  |  | |   | | |            | |       
AACATATAGGAACAAAGACTGCTGTGCAAATCAGAAGTCATGCACAAAAATTCTTT-TCAAAGgtcaatcgataccttctaactttatgcttattgtataaatatatctttgtttcttattgcttggtaatatttctatataataaaacaaactgatgttcat

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|29643682|gb|CB648689.1|CB648689
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58665197|gb|CK053883.1|CK053883
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58665214|gb|CK053900.1|CK053900
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29613821|gb|CB618834.1|CB618834
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|13904796|gb|BF889434.1|BF889434
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29629255|gb|CB634266.1|CB634266
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58663892|gb|CK052578.1|CK052578
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29674993|gb|CB671268.1|CB671268
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29624811|gb|CB629822.1|CB629822
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|33676435|gb|CF304674.1|CF304674
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|33675928|gb|CF304167.1|CF304167
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29676888|gb|CB673163.1|CB673163
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58663489|gb|CK052175.1|CK052175
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29622092|gb|CB627103.1|CB627103
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58605207|gb|CK033240.1|CK033240
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29630692|gb|CB635701.1|CB635701
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29613863|gb|CB618876.1|CB618876
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|58653962|gb|CK042642.1|CK042642
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29677851|gb|CB674126.1|CB674126
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
EST: gi|29628510|gb|CB633521.1|CB633521
EST:     CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG                         TTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC
genomic: CAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGAC

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: 67 (upstream exon), 73 (downstream exon)
Score: 312

AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctc ... aatattacagTTGGAAAAGGAAGCTATCAACAATGGCACTTCTCCAGGACAAGCTCATGACATCGACATACCTCCACCACGACCAAAAAGAAAACCTAACAGTCCATATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAGgttcttcctctatcttattggccagtgctcctttttttggtttagcgctatctccttagctttctggtttccttgtctttacctttgggataaaaacggc

- - - - - - - - - CAGCTG
- - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - AGAAGT