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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG

Basic information

species Oryza sativa
transcript LOC_Os03g54920.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G123732_T01 (Zea mays), 3'ss of exon 4
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttata-tagcttttctt--catcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG
        ||| |||||   |||| |   |||   || | |||||   |||  |  | | || | |  ||||  |       |    ||| || | |  || |||  | |||   ||   |  |  || | |  |||||||||||||| ||||||||||||| ||| ||||| || || ||||| || |||||||||||||||||||||||||||| ||| |  | |||  |||  ||||
--------gtaccttcttgcctatga---tat-gttatgttgcttctgtgaagtgctgctttcgtagcttcttagcttgtgttgtgccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG

upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G086497_T01 (Zea mays), 3'ss of exon 6
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattggga---tattctacgtaccctcttgttcttatatagcttttctt-----catcaaaaattgctggttcatgtc-tgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG
        ||| |||||   ||||  || | | ||| |||| || | | |  ||| | | || |     || | |  ||||     |     | | | |||| |  |      ||      |||||| || || || |  || ||||||||||| ||||||||||||||||||||||| || || ||||| || ||||||||||| |||||||||||||||| ||| |  | |||   || |||||
--------gtaccttcttgcctat-gacctgtcacttcgcttctgtgtagtgcttcttccttagttccttagtttgtgtactggtataactgtctgtggcttgtaatgaaattatttgtcgttgctgatttatttcgtatgtttagGAGGAAGACATGCTCCTAGAGAACGTCTACTATTCTGAAATGAAGGATGCTGGGTTCTTCGATGCTGACTGGGATTAATCCGTGGCTACTGTGCTGTATG

upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G00490.1 (Glycine max), 3'ss of exon 6
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG-
                                                             |  || | |||    |   |  ||||  | | | | ||||      |    ||      |  ||       || ||||||| ||| | ||  | || ||||  || ||||| ||||||||||| || || |||||||||||||||||||| | ||   |  | |  |      ||| 
------------------------------------------------------------gtaaga-actcttttgatattactgtttctttctggtttttagaatacgtgcatgaacattatattatgtgctgcagGAGGAGGATTTCCTTTTGGACAACGCATATTACTCCGAGATGAAAGATGCCGGATTCTTTGATGCTGACTGGGAATAATTC-CTCAAAAAATTATACATGG

upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G08560.1 (Glycine max), 3'ss of exon 5
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG-
                                                             |  || | |||    |   |  ||||  | | | | |||| |    |    ||         ||       || ||||||||||| | ||  | || ||||  || ||||| ||||||||||| || || |||||||||||||||||||| | ||   |  | |  |      ||| 
------------------------------------------------------------gtaaga-actcttttgatattactgtttctttctggtttttataatacgtgcatgaacatcatattatgtgctgcagGAGGAAGATTTCCTTTTGGACAACGCATATTACTCCGAGATGAAAGATGCCGGATTCTTTGATGCTGACTGGGAATAATTC-CTCAAAAAATTATAAATGG

upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattg---ctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATAC-CACGCCGTATG-
     |  | || | |    ||  |||    || ||  | |  ||  ||||  |  |   |||    |||| | |||      | || |   || | ||   |||   | |  ||    |||| |    | |||    ||||||||||| |||   | ||||| || |||||||| ||||||||||| || || |||||||||||||| ||||| ||||  |||  | | |   | | ||  
--gtcatcggatgtccatcccttgcaa---gttcctctgttatttctttgaaatc-tgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGAT--GCAACTGCACTTTCTGAATCA

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|86490061|gb|CI132694.1|CI132694
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|86835747|gb|CI348204.1|CI348204
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88298341|gb|CI561134.1|CI561134
EST:     TTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: TTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88543335|gb|CI473334.1|CI473334
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88268961|gb|CI380259.1|CI380259
EST:     TTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: TTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88202487|gb|CI200842.1|CI200842
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTTCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88554329|gb|CI484502.1|CI484502
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|86542850|gb|CI183056.1|CI183056
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTTCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|87008567|gb|CI315025.1|CI315025
EST:     CTCTTTACCTTCCACTTCTGTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|86892806|gb|CI312118.1|CI312118
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88511282|gb|CI438788.1|CI438788
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|55438101|gb|CV732344.1|CV732344
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88962251|gb|CI097404.1|CI097404
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|86543258|gb|CI183464.1|CI183464
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88559941|gb|CI490561.1|CI490561
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTTTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|66912726|gb|CX099574.1|CX099574
EST:     CTTTCCTGGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|86863609|gb|CI345283.1|CI345283
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
EST: gi|88522143|gb|CI449880.1|CI449880
EST:     CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG                         GAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT
genomic: CTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCT

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: 61 (upstream exon), 69 (downstream exon)
Score: 9

GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggt ... ctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG
                       atcaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATACCACGCCGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT