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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

Basic information

species Oryza sativa
transcript LOC_Os04g52361.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G019325_T01 (Zea mays), 3'ss of exon 2
gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
||  |    |  |||  |||| ||   || | | ||   | |||| ||||  | |  |  ||||| |   |||||  |  |||||||||||||||| ||||||||||||||||||||||| ||||||||||| || || |||||||||||||||||||| |||||||||||||||||||||||||||
gtgagagattcttgcctcttccatgctttctattct---cagtgaacaatatagattttgtgacagtagatttcttttaaattttagCTCAAAGAAATCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAATCGATTTTGGAAGAGCATTGGCCTTGGTTTCAAGACTCCCAGGGAAGCAATTGAA

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
||  |    |  |||  |||| |     |   | | ||| | ||||||||  |||  |  ||||| |   | |||   |  || |||||||||||| || ||||| ||||||||||| || ||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
gtgagaactttttgcctcttcca-----tgctttcaattttctgagcaatatacattttgtgacagtagatatcttaatt-ttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G23400.2 (Glycine max), 3'ss of exon 2
------gtagggttctgc----tgctcc--ttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaat-gtt-tttctgcttgatttt--agCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
       ||| ||||       |||| |  ||   |   || |||  | | |  || |   ||   | |      |  | ||| ||| || |   |||   ||| |||||||| |||| ||||| ||||  || || || ||||| ||||| || ||||||  |||||| ||||| || ||||||||||||||||| || |||
gtacgcttagtgttcgagaaaatgcttcacttttgttgtttttgttttttccattgtgatgttttgatgctgaatcgtttgttgtttttggtccctttcgcagCACAAAGAAGACTGGGAAGGGAAAGAGACCTGGAAAAGGTGGGAACCGCTTTTGGAAGTCCATTGGGCTTGGATTTAAGACTCCCAGGGAAGCCATCGAA

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagggt--tctg--ctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
|||   |  ||||  |   ||    ||||   |   | | |||     | | ||||| | |  || |   | ||||| ||  || ||| ||||| ||||  ||||| || || ||||  || ||||| ||||| |||||||||||||||| ||||||  | || |||||||||||  | ||||| ||||| 
gtaaattcatctgaacaaatctgagaatcttattacttccatttacaaatcgattcatatgattt-atgttttttttttgtgtg-tttcagCTCGAAGATATCTGGGAAAGGAAAGAGACCTGGTAAAGGTGGAAACCGTTTCTGGAAGAACATTGGTTTGGGTTTCAAGACTCCTCGTGAAGCCATTGAT

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagggttctgctgctccttcaatcaattatgtactattc---tgtgagcaattcacacgtc-ttgacaatgttt-ttctgcttgatttt---agCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
|||   ||  | | |   |||  ||  || | || | ||    |||    || |  || ||  || | | ||||  || |   ||||||    ||||| ||||| ||||| ||||| ||||  || || || ||||| |||||||||||||||| ||||||  | ||||||||||||||  | ||||| ||||| 
gtaattttgcgattcgatttctctctgttctctattgtttcattgtatttaagttccaagttgtttatattgttcattgtttctgatttatcaagCTCGAAGAAATCTGGAAAGGGAAAGAGACCTGGAAAAGGTGGAAACCGTTTCTGGAAGAACATTGGTTTGGGCTTCAAGACTCCTCGTGAAGCCATTGAT

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G30800.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
|||   |    |  |||    | |||| |   |  |||| ||   || ||   | | |  ||   ||| ||       |  | | ||||| ||||| ||||| ||||| |||| ||| ||||| || || || ||||||||||||| |||||||||||| ||||| ||||| || || || ||||||
gtaat-tgtcacacctcaaaaattcaactgctttgtattttg---gctatggtctctttatgcttatgattcaa-atgttctatcagCTCGAAGAAATCTGGTAAGGGAAAGAGGCCTGGTAAAGGAGGTAATCGTTTCTGGAAGAACATTGGCCTTGGTTTCAAAACTCCAAGAGAGGCTATTGAA

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 2
---------gtagggttctgc-tgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgc----ttgatttt---agCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
          |||   |  |  |  | |     |   | |||   |  |  ||| |  |||     ||||| | | | | ||  ||     ||||  ||   ||||||||||||   || ||||| |||| ||| || |||||||| || || |||||||||||||||||  | || || ||||| ||||| || |||||||||
atatacctaatagaacttggaatatttcccttttttttcatg-gttgataagtgtgtcatttgt--gtcttaa-agtatcttaatgagcaattgaactttgcagCTCAAAGAAGGGCGGAAAGGGAAAGAGGCCTGGAAAGGGTGGAAATCGATTCTGGAAGAGCATTGGATTGGGATTTAAGACACCCAGAGATGCAATTGAA

upper sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgc-ttgat-----tttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
                            | || || || |  | |        || |   | | || |        || |  ||| || ||  | ||| ||||   |||      |  ||||| ||||| ||||  ||||| |||| ||| || |||||||| ||||| |||||||||||||||||| | || || ||||| ||| | || || ||||||
gtaacagaaaattacgaatacattctcattggtttttgttttttcccttggggatgac--attgtttttcccctttttaattcgtttttaccgtttttctctgtgctgaaaacaatccagCTCGAAGAAATCTGCGAAGGGGAAGAGGCCTGGGAAGGGTGGAAACCGGTTCTGGAAGAGCATTGGCTTAGGGTTTAAGACACCCCGAGACGCTATTGAA

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|88670225|gb|CI723473.1|CI723473
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|87026526|gb|CI252480.1|CI252480
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88414388|gb|CI691548.1|CI691548
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88578563|gb|CI687500.1|CI687500
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|4716480|gb|AU057596.1|AU057596
EST:     CAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: CAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88673013|gb|CI727128.1|CI727128
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88670002|gb|CI724118.1|CI724118
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88576375|gb|CI670520.1|CI670520
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|87030607|gb|CI255036.1|CI255036
EST:     TGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: TGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|38474928|gb|CF959061.1|CF959061
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|86822694|gb|CI251785.1|CI251785
EST:     GCAGACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: GCAGACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|33660458|gb|CF291425.1|CF291425
EST:     GAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: GAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|3763186|gb|AU029938.1|AU029938
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88670956|gb|CI725072.1|CI725072
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88303277|gb|CI668925.1|CI668925
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88665722|gb|CI715878.1|CI715878
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88665678|gb|CI715834.1|CI715834
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|5005510|gb|AU070275.1|AU070275
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
EST: gi|88669454|gb|CI723372.1|CI723372
EST:     ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT
genomic: ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTT

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: 41 (upstream exon), 75 (downstream exon)
Score: 228

ACTGAGAAGGCATTCCTGAAGCAGCCAAAGGTTTTCCTCAGgtagggttct ... ttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
                                    tttttctgctt  CT-rich tract
                                aatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA