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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtcatgttttcttaaattgtgttaactcatcattctcttctcattgttttttacaatttaatatagtaaatctctttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 7
gtatggtcatgttttcttaaattgtgttaactca-tcattctcttctcattgttttttacaatttaatatagtaaatctctttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG
||||| |    | | || ||||  | | |||| | | |   |  |    |   | |||  |  ||   |||     ||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||| ||||| ||||||||||||||||| |||
gtatgcttgcctctactcaaatcctctcaactgaattaagattattaattcactgtttgaagcttttcatatagtttctctttctgccagCCTGCACAGATTGCTGGATGCAAAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAG

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 4
--------------------------gtatggtcatgttttcttaaattgtgttaactcatcattctc--ttctcattgttttttacaatttaat--atagtaaatctctttct--gccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG
                           | | ||  |||| ||     |   |||   |  | ||| |   |  ||||  | ||||   ||||  |  ||  |  ||   ||| |  |||||||||||||||||||||| || |||||| |||| ||||| || || ||   ||  |||||||  ||||| |||
gtaagttgaattgatgtctaactagtttgtagtattgttctccatcctatagttgcattgtgattgttgataatcatcatctttttggattttgttgatctttgattgttttatatgccagCCTGCACAGATTGCTGGATGTAAAACTATTGTCCTTGCAACTCCTCCAGCTCAGGATGGTACTATATGCAAG

upper sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------gtatggtcatgttttcttaaattgtg--ttaactcatcattctcttctcattgttttttacaatt---taatatagtaaatctctttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG
                                    |  | |||| ||     ||||  |   |||  || ||    |  |    |   ||   ||| ||   | | || |   || |  |    ||||||||||||||||||||| || || |||||||| ||||| || ||||||||||  |||||  |||| || |||
gtaggttgatcaaatttaccaagtcaattgccttttttagttcatcttcctacaaatctttatttagatcctcgactttgtgatgtctgttgccacatttgattgacattgagtatgttctgtcaccagCCTGCACAGATTGCTGGGTGTAAGACTGTTGTCCTTGCAACTCCCCCTAGTCAAGATGGCGGCATCTGCAAG

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|32948183|gb|BP184755.1|BP184755
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|29680232|gb|CB676507.1|CB676507
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|29685418|gb|CB681693.1|CB681693
EST:     CTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: CTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|88422364|gb|CI689178.1|CI689178
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|58678012|gb|CK066699.1|CK066699
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACGGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|117232645|gb|CT842234.1|CT842234
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACGGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|58673757|gb|CK062443.1|CK062443
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACGGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|29683233|gb|CB679508.1|CB679508
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|29662201|gb|CB658476.1|CB658476
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|58666767|gb|CK055453.1|CK055453
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACGGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
EST: gi|88583475|gb|CI700958.1|CI700958
EST:     TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTG                         CCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT
genomic: TCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGT

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: 75 (upstream exon), 72 (downstream exon)
Score: 25

TGTAAGATGTAAAAGAATAACAAGATGCATTGGTTCTGTTGGCCTTTATGTCCCAGGTGGCACTGCAGTATTGCCTTCCACTGCATTGATGCTTGCTGTGgtatggtcat ... tttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctcttctcattgttttttacaatttaatatagtaaatctctttctgccagCCTGCACAGATTGCTGGTTGCAAAACTGTTGTTCTTGCCACACCCCCTAGTCGTGATGGTAGCATATGTAAG
                          atttaat  putative branch site (score: 25)
                                         tctctttctgcc  putative PPT
             attgttttttacaatt  TA-rich tract