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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaggagtaagctcggtggcacttaagcaaaacagtgcttaagttaatatgcacaataattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64630.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64630.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G053284_T01 (Zea mays), 3'ss of exon 1
ccaggagta--agctcggtggcacttaagcaaaacagtgcttaagttaatatg-cacaataattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG
   ||  ||  |   | | |||            |  |  |   ||| |  || | | ||      |||    ||  |  | || ||  |   | || ||||||| |||| |||| ||||||||||||||| |||||||  |||| || |||||||||||||||||||| |||
---ggtttaccattgcagcggcggcggcatgcttcttttgtggggtttacctgactccatggacactttaacgattaacaccgagtatagcattctgctgcagAA-CACT-GAGGAATGGCTGAAGAGGATGTCCAGCCCCTTGTGTGCGACAATGGCACTGGAATGGTTAAG

upper sequence: LOC_Os01g64630.4 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 1
ccaggagtaagctcggtggcacttaagcaaaacagtgcttaagttaatatgcacaataattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAAG---AGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG
   | | | |      |  ||   | | ||| |   | || | | |  | |     |   |  || | ||      |    ||  | || ||| |    | |   | |     ||||| || |   | || || || |||||||||||||||||||| ||||||||||| |||
attgaattgaatctact--catgaatgaaaagcctggtttgattaagcaagtgttttcggtt-ttctcgatcaagattcagatctttatgtttttgattgcagATCGTAGACCATGGCCGATGCTGATGACATTCAACCTATTGTCTGTGACAATGGTACTGGAATGGTTAAG

upper sequence: LOC_Os01g64630.4 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 1
ccaggagtaagctcggtggcactt--aagcaaaacagtgcttaagttaatatgcacaataattgatttttgaatgcattctgaatac---tgatatttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG
     | ||| | | |     |||  || | ||   ||| |    ||  | |  ||   |   | || |  ||| ||||  |  | |   | |  ||| ||  ||  | |  ||   |||||     |||||||| |||||  |||||||||||||||| ||||||||||| |||
-----aataaacgctgctaatcttcgaaactaagttgtgatctgattcgtgtttacttcatgagcttatccaattcatttcggtttcattttactttttttttagTGAAAAATGGCCGATGGT----GAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: LOC_Os01g64630.4 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 2
ccaggagtaagctcggtggcacttaagcaaaacagtgcttaagttaatatgcacaa--taattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAA---GAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG
  | |   |   || |    |  |||  |    | |  ||  || ||   ||| ||  |||    | ||  | |   | |       | |||||| |     |   | |  | ||||||| ||    || |||||||||||  | |||||||||||||| ||||||||||| |||
--atggaaattatctgaaaaagctaaaaaggtgaatattt--gtcaagcagcaaaacttaaactttgttatactttgtcccctgacttcatatttctcatgcagGTAATAAAAGGATGGCCGATACTGAAGATATCCAGCCCCTCGTCTGTGACAATGGAACTGGAATGGTGAAG

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|29658476|gb|CB654751.1|CB654751
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88334366|gb|CI642611.1|CI642611
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88732645|gb|CI755822.1|CI755822
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88741930|gb|CI764435.1|CI764435
EST:     TCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: TCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88303237|gb|CI668885.1|CI668885
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|13807445|gb|AU181959.1|AU181959
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|86883922|gb|CI309176.1|CI309176
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88732446|gb|CI755623.1|CI755623
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88312389|gb|CI584912.1|CI584912
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88825649|gb|CI776214.1|CI776214
EST:     ATCTATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88325169|gb|CI646589.1|CI646589
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|33693145|gb|CF321384.1|CF321384
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATTCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88338591|gb|CI656892.1|CI656892
EST:     GATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: GATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88342907|gb|CI640240.1|CI640240
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|29613794|gb|CB618807.1|CB618807
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88825669|gb|CI776234.1|CI776234
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88290474|gb|CI665263.1|CI665263
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88307092|gb|CI640526.1|CI640526
EST:     GATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: GATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|88348188|gb|CI637649.1|CI637649
EST:     ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGT                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: ATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
EST: gi|4714771|gb|AU055888.1|AU055888
EST:     CCGCCGATCGCCTCGCCGAAGTCTCCGA-G-                         AAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA
genomic: CCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAA

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: 44 (upstream exon), 70 (downstream exon)
Score: 6

GCGTCAGCGGCGGAGCTCTCTAGAAGGAGCAGAGGAGTCCCCCCCAAGCGATCGATTCGATCCCCTCCGCCGCCGATCGCCTCGCCGAAGTCTCCGAGGTgtaagcccgt ... tttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgcacaataattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG
                                     tactgat  putative branch site (score: 6)
         aataattgatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaggagtaagctcggtggcacttaagcaaaacagtgcttaagttaatatgcacaataattgatttttgaatgcattctgaatactgatatttgttgcagAAACACTTGAGGGATGGCTGAAGAGGATATCCAGCCTATTGTCTGTGACAATGGCACTGGAATGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT