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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag...

Basic information

species Oryza sativa
transcript LOC_Os03g36750.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 5
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagtt-attttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag---
||||| |||||||| || |  ||| |||| |||||| | || || || |||||||||||||||||||||||||||||||  ||||||||||| |||||||||| ||||   | || || |||  ||||    || || | ||  | |  ||  |   ||||| |     |||   |    |  ||  ||   |||     
GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgatttcacagtttaacaaactctaagc--attaatccat-ctttccctgttgagttatgtgccatcaaagggtccttatatg-gtatcacattactg

upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G18320.1 (Glycine max), 5'ss of exon 6
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatag-ggcatag---
|| || |||||||| ||||  || ||||| |||||  | ||||||||||| |  |||||||| ||||| |||||||| |||||||| ||||||||||||||  ||||  |  ||| |    || |       |    ||  |  | ||| |  | ||| |    ||    ||| |   |   || |||    |||     
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCAgtaaga-atttcatccttctaatgttaatttggtagttttccagcacacaatcaaaatatttgtt---agtcctattttacggccctgcatattaacattccgt

upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 5
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag-
|| || |||||||| ||||  || ||||| |||||  | ||||||||||| |  |||||||| ||||| |||||||| |||||||| |||||||| |||||  ||||  |  ||| |    || |       |    ||  |  | ||| |  | | | | |    |     |    |    | |  |      |  
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaaga-atttcatccttctactgttaatttggtagtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt

upper sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 5
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatca----aacaat--attctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag
|| || |||||||||||||| || ||||| ||||| || ||||||||||| |  |||||||| || || ||||||||||| ||||| |||||||||||||   | |||| |   || | |||  | || |  |||    ||| |   |||| |  ||  | || |||     |     | ||  | ||   | | || |   
GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCAgtaa---acttttcatcccacttaatgttgatgcagtcagtgtaaccactcattcaacttaaatgttcatgtagtcagttgct-ttctggagaccacatggaag--

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|33684374|gb|CF312613.1|CF312613
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|29625469|gb|CB630480.1|CB630480
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTTGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|38473540|gb|CF957672.1|CF957672
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|33797557|gb|CF324638.1|CF324638
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|117242305|gb|CT842941.1|CT842941
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|29657434|gb|CB653709.1|CB653709
EST:     AATTACCATATTTGCTGGAGATGTGGTTCCTCGTNNNNNNNCCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAA-CCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|29657435|gb|CB653710.1|CB653710
EST:     AATTACCATATTTGCTGGAGATGTGGTTCCTCGTNNNNNNNCCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AATTACCATATTTGCTGGAGATGTGGTTCCTCGT-AAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|38475316|gb|CF959449.1|CF959449
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|58586453|gb|CF984761.1|CF984761
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|88257860|gb|CI360446.1|CI360446
EST:     TCGTAGAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATGCTAG
genomic: TCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCAT-CTAG
EST: gi|38478320|gb|CF962453.1|CF962453
EST:     TTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAAGCTGACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: TTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCT-ACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
EST: gi|29687538|gb|CB683813.1|CB683813
EST:     AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA                         GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
genomic: AAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG

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: 73 (upstream exon), 47 (downstream exon)
Score: 46

GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttatt ... atctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa