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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtcctgacattcccaacttgtaaactcttccctcgccatttcaaacacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG

Basic information

species Oryza sativa
transcript LOC_Os06g07760.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007683_T01 (Zea mays), 3'ss of exon 3
gtaagtagtcctgacattc----ccaacttgtaaactcttccctcgccatttcaa-acacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG------
||  |||||||     | |    | || | || |    | | ||| | ||||  | |   ||| || |||  ||  | ||||| | |||||||  | ||||||||| || |||||||| |||||||| ||||||||||||||||| |||||||| || |||||||||||||| || || ||||| || |||||||| ||      
gtgggtagtccaagattccagaacgaattagtcactcatgctctcactatttggagatctagatccatttttctcgtcctgaatattctcctgtgtgatcttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCGCTGCAAAGTTCGCCGTGGGACAAAGGAAACACTGAGGCGAGA

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173911_T01 (Zea mays), 3'ss of exon 4
gtaagtagtcctgacattcccaacttgtaaactcttccctcgccatttcaa-acacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG------
||  |||   || | |||||  |      || |  || ||||   | |||  |    ||    |    |  ||  | |      ||||| ||  | |||||| || |||||||| |||||||| ||||||||||||||||| |||||||| || |||| || |||||| |||||||| || || |||||||| ||      
gtgggta-ctctaagattccaga---acgaattagtcactcgtgctgtcactatttggaggtctagatccatttttcagg----tcctgaatatttttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCACTACAAAGTTCGTCGCGGTACAAAGGAAACACTGAGGCGAGT

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007683_T02 (Zea mays), 3'ss of exon 3
gtaagtagtcctgacattc----ccaacttgtaaactcttccctcgccatttcaa-acacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG
||  |||||||     | |    | || | || |    | | ||| | ||||  | |   ||| || |||  ||  | ||||| | |||||||  | ||||||||| || |||||||| |||||||| ||||||||||||||||| |||||||| || |||||||||||||| || || ||||| || |||||||| ||
gtgggtagtccaagattccagaacgaattagtcactcatgctctcactatttggagatctagatccatttttctcgtcctgaatattctcctgtgtgatcttcagGCTTCTCTGGATGCCACCGCTACGAGGCTCACCAGCGCCTTGGTCTCCCAACCATCCGCTGCAAAGTTCGCCGTGGGACAAAGGAAACACTGAG

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G02350.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------gtaagtagtcctgacattccca--acttgtaaactcttccctcgc---------catttcaaacacagaaccgtttcccttt--tgctgaaaactctcctg--cattatcttc-------agGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG----
                                                                              |   |   | || | |   |  ||||| ||  ||| || |              |||  || |   | || |  |   |   ||  |||||      ||  | |||||||        |||||| || || |||||||||||||||||||| |||||||| || ||||| || ||||| |||||| | || || || || ||||| ||  ||||    
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTA

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G02350.2 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------gtaagtagtcctgacattccca--acttgtaaactcttccctcgc---------catttcaaacacagaaccgtttcccttt--tgctgaaaactctcctg--cattatcttc-------agGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG------
                                                                              |   |   | || | |   |  ||||| ||  ||| || |              |||  || |   | || |  |   |   ||  |||||      ||  | |||||||        |||||| || || |||||||||||||||||||| |||||||| || ||||| || ||||| |||||| | || || || || ||||| ||  ||||      
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAGGTTAGT

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G02350.3 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------gtaagtagtcctgacattccca--acttgtaaactcttccctcgc---------catttcaaacacagaaccgtttcccttt--tgctgaaaactctcctg--cattatcttc-------agGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG
                                                                              |   |   | || | |   |  ||||| ||  ||| || |              |||  || |   | || |  |   |   ||  |||||      ||  | |||||||        |||||| || || |||||||||||||||||||| |||||||| || ||||| || ||||| |||||| | || || || || ||||| ||  ||||
gtatgtgttttttttggattgtgtatggaatcttataattattattacataacttggtcatgctcatagctaaaaaacagtaaaatcagaaacttgaaggacttgaaagatctaccatgatggaataacttgttttcaagatccatccatgccttctcactgtggaaaatcaatatgtcctttatctttggtttgtagGTTTCTCCGGCTGTCACCGCTATGAGGCTCATCAGCGCCTTGGACTCCCCACCATCCGTTGCAAAATACGCCGGGGTACAAAAGAGACTTTAAG

upper sequence: LOC_Os06g07760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0011g01620.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------gtaagtagtcctgacattccca-acttgtaaactcttccctcgccatttcaaacacagaaccgtttcccttttgctgaaaactctcctgcattat----cttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG
                                                                     | |  ||   |   |||||    | ||    |     |       |  |    || | | ||  |||   |       |  ||  |||||  | |    || |||||||||| || ||||| || || || || |||||||||||||| ||||| || || || |||||||| || || || |||||||||||| | ||
gtatgtgtttattcatatctttactatagttcttctatctagttcacaatatttagtgatctgtcggtaggatttaactcctccattcttttaattaaggaaaaaacttgaaataacttctgcagaaatcctgttcagctgaagctcatgcttccctgctctttgagactgcagGTTTTTCCGGTTGTCATCGGTACGAAGCACACCAGCGCCTAGGGCTCCCAACAATTCGTTGCAAAGTTCGACGAGGAACGAAAGAAACATTGAG

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|87031893|gb|CI268122.1|CI268122
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|88664093|gb|CI490467.1|CI490467
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|25798058|gb|CA754019.1|CA754019
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|117232192|gb|CT859987.1|CT859987
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|88273375|gb|CI393781.1|CI393781
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|88324654|gb|CI506038.1|CI506038
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|56158131|gb|C73488.2|C73488
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGG
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGG
EST: gi|86841916|gb|CI337538.1|CI337538
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|5005508|gb|AU070273.1|AU070273
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGG
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGG
EST: gi|88567828|gb|CI498545.1|CI498545
EST:     ATTGACGTACTGGAGGTTGATGGAGTTTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGTTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|88567353|gb|CI498070.1|CI498070
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|88569011|gb|CI499728.1|CI499728
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|38477761|gb|CF961894.1|CF961894
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
EST: gi|58592631|gb|CF990939.1|CF990939
EST:     ATTGACGTACTGGAGGTTGATGGAGTCTACTATG                         GTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA
genomic: ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGA

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: 34 (upstream exon), 66 (downstream exon)
Score: 13

ATTGACGTACTGGAGGTTGATGGAGTCTACTATGgtaagtagtc ... ttatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaaacacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG
                                             ttatcttc  CT-rich tract
                                            attatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtcctgacattcccaacttgtaaactcttccctcgccatttcaaacacagaaccgtttcccttttgctgaaaactctcctgcattatcttcagGTTTTTCTGGATGTCACCGCTATGAGGCTCACCAGCGCCTAGGTCTCCCGACTATCCGCTGCAAAGTCCGTCGCGGGACGAAAGAAACACTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA