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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtaaatttgtttctcatgtggctattagctggactttaagcaagtattgttcctatgctattgtttgtggatatggcagtttgatttgcacctgcaattttatttaattgtgctgtagtcctaattattttctacttgctctgatgatcttgttttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCACAGAAAAAGCAGCATAT

Basic information

species Oryza sativa
transcript LOC_Os11g33330.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 7
gtcagtgtaaatttgtttctcatgtggctattagctggactttaagcaagtattgttcctatgctattgtttgtggatatggcagtttgatttgcacctgc-aattttatttaattgtgctgtagtcctaattattttctacttgctctgatgatcttgttttaatgaca-----gATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCACAGAAAAAGCAGCATAT
                                                                        | | | ||  || |||||        |   || | |  |   |   |  |||||     ||  |   |||||| |||||||       |  | |  ||     |||||| ||||||||||||||||||||||| || ||||||   || || || || |||||  | ||| |
------------------------------------------------------------------------gagcacatctcattttgaaaaaaggttattaaatatcctctgtaacgtagtagtt----ttgctccatacttgttctgatgtctcccctccacttccaattcagATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT
















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|58665341|gb|CK054027.1|CK054027
EST:     TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAG                         ATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
genomic: TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
EST: gi|58663678|gb|CK052364.1|CK052364
EST:     TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAG                         ATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
genomic: TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
EST: gi|33794779|gb|CF323269.1|CF323269
EST:     TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAG                         ATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
genomic: TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
EST: gi|66922750|gb|CX109598.1|CX109598
EST:     TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAG                         ATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
genomic: TTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
EST: gi|88574886|gb|CI666655.1|CI666655
EST:     TTGTGCAATACCTGGCTTGGCTTGACAATCAG                         ATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA
genomic: TTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCA

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: 64 (upstream exon), 68 (downstream exon)
Score: 69

AATCCCGTGGAGCTGGATGGTTTGAGGAAGGCACATATTCGAGATGGTGCTGCTGTTGTGCAATACCTGGCTTGGCTTGACAATCAGgtcagtgtaa ... ttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCACAGAAAAAGCAGCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgtagtcctaattattttctacttgctctgatgatcttgttttaatgacagATGCAAGAGAACTATGGAGCTTCTGGTTACTTTAGTGAGGCCAAGGGATCACAGAAAAAGCAGCATAT
                                      tcttgtttt  CT-rich tract
            taattattttctactt  TA-rich tract