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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttccttgtaaaagtactgttttattttgatgctgtgagtacactgtacactatgttttctaattttctgaagttaatatttacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 7
cttttccttgtaaaagta-ctgttttattttgatgctgt-gagtacactgtacactatgttttctaattttctgaagttaatatt-tacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA
 |  |  ||  | | | | ||| | |     |||| ||| ||  | |  |  ||  |  |||| ||   |   ||   | || |  |  | ||  |  ||||||| |||||||| |||||||| |||||||| ||  || ||||||||||||| |||||||| || ||||| || ||||||||| | ||||||||||| || 
ttacttttttcacacggatctgctatgcacggatgttgtagaacagagggagcaaaaaatttttta---tcaagattctcatgtaatgatcttttcgtttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGCTGCAGTCATGATGCGCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG

upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 3
cttttccttgtaaaagtactgttttattttgatgctgtgagtacact-gtacactatgttttctaattttctgaagt-taatatt-tacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA
        || ||     |||       |  ||       ||| |   |   |  |  |||| || |  ||   | | | || |  || ||||  || ||||||| |||||||| |||||||| |||||||| ||   | |||| |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| || 
---agtagtggaatgaggctggaacccatcaatatcacttgtagagaaggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG
















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|38473913|gb|CF958045.1|CF958045
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29675062|gb|CB671337.1|CB671337
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|218481593|gb|FG960934.1|FG960934
EST:     ATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: ATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTCCAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|86500993|gb|CI143626.1|CI143626
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|38481075|gb|CF965164.1|CF965164
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTGTTGGGAGACATGCTGCTTGATAGATCCAACTCTGCAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29679531|gb|CB675806.1|CB675806
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|87008328|gb|CI301086.1|CI301086
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|58663168|gb|CK051854.1|CK051854
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|25799534|gb|CA755495.1|CA755495
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTGTTGGGAGACATGCTGCTTGATAGATCCAACTCTGCAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|58688748|gb|CK077435.1|CK077435
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: CTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
EST: gi|58674983|gb|CK063670.1|CK063670
EST:     TAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCCAGGCTATCAAG                         TTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT
genomic: TAGGTTGCTATCATCAACCAACTACATAACAAAAAGGC-AGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGT

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: 69 (upstream exon), 70 (downstream exon)
Score: 140

TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAGgtattgctat ... cccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtacactatgttttctaattttctgaagttaatatttacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA
                                  tatttacttttccccc  CT-rich tract
            ttttctaattttctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttccttgtaaaagtactgttttattttgatgctgtgagtacactgtacactatgttttctaattttctgaagttaatatttacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA

- - - - - - - - tactgtt
- - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - -ctgtaca