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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcgtttgctcacttaataggtagtagccatcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA

Basic information

species Oryza sativa
transcript LOC_Os02g10640.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 5
gtgtg-tcgtttgctcacttaataggtagtagccatcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA
||||| |  ||| ||   || || || | |    || | ||| ||   || |||   ||  |    |||| |    ||||||||||||||||| ||||| |||||||| ||||||||||| ||||| || |||||||| |||||||||||||||||||||||||| |||
gtgtgattttttacttcattgat-ggcattcagtatttcttataattcaaatatggcttaca----taatgtctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 5
gtgtgtcgtttgctcacttaataggtagtagcca-tcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA
| ||||   ||  |||||| || | | |||  || | |||   |  ||    ||   |||     |||||      ||||||||||||||||||||||| || ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||||||||| || |||
gcgtgtgactt-ttcacttcattgatggtattcagtatttcttatccttcagatatgttgcttacataatgcctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA
















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|163917943|gb|EG715243.1|EG715243
EST:     GTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: GTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|58686072|gb|CK074759.1|CK074759
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|300215978|gb|HO088604.1|HO088604
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|86905949|gb|CI292480.1|CI292480
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|218493541|gb|FG956814.1|FG956814
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|2310656|gb|C26811.1|C26811
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACAT
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACAT
EST: gi|218480375|gb|FG953360.1|FG953360
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|58662318|gb|CK050998.1|CK050998
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|58599209|gb|CK009737.1|CK009737
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
EST: gi|86829542|gb|CI286737.1|CI286737
EST:     CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATCGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG
genomic: CACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTG

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), 75 (downstream exon)
Score: 73

GGTGTTCTACTCTATGGTCCACCAGGAACTGGTAAGACACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgtcgtt ... ggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagccatcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA
                                 tactgat  putative branch site (score: 73)
          ttttacaaactaatta  TA-rich tract