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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgttgcttttaccttatctttttaagcggttgaattcccttttctaaattattcagtgcctggaagcaaccattgccatcacttcttttgaaaaatagttacaaatgcgaaaccctctttacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGACCCCCATGTCAGCGAATTCCTGTACGAGAAAGCTAGCACAAAAGACAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g49380.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49380.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085438_T01 (Zea mays), 3'ss of exon 7
gtcagtgttgcttttaccttatctttttaagcggttgaattcccttttctaaattattcag---tgc-ctggaagcaaccattgccatcacttc--ttttgaaaaatagttaca---------------------aatgcgaaaccctcttta--------cttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGACCCCCATGTCAGCGAATTCCTGTACGAGAAAGCTAGCACAAAAGACAAGA
|||| | ||||||  || ||  ||  |  | | |  ||  || || || |  ||  || |    ||  ||||| ||||    ||  | |||| |  |||||     ||  ||||                     ||  | ||| |   ||||        ||  | |||| |  || |||||||||||||| |||||||| |||||| |||| ||||| || || |||||| ||||||| || |||||||| ||||| || |||||||
gtcactattgcttgcacttttgctcatggatctg--gatctctctgttttgtatcgtttaaacatgttctggatgcaagtcatgagaccactgcgtttttgtttggtatgtacattccttctcgttgaagtacctaacacaaaaacacttttatgatattcctatatagATCTCCTCTCCATTGCTGATTCTTCACGGAGCCGCAGACATGGTAACCGATCCTCAGGTCAGCAAATTCCTTTATGAGAAAGCCAGCACGAAGGACAAGA
















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|163918635|gb|EG710317.1|EG710317
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
EST: gi|86835208|gb|CI346683.1|CI346683
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGGTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
EST: gi|27548274|gb|CA767490.2|CA767490
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
EST: gi|3107506|gb|D43246.1|D43246
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
EST: gi|3107548|gb|D43288.1|D43288
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGNATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
EST: gi|3107521|gb|D43261.1|D43261
EST:     CAGTTGAACTTTTGAAGGCTACAAAGGACATAGCATCCCAGTTGGAGAAG                         ATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC
genomic: CAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGAC

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: 30 (upstream exon), 65 (downstream exon)
Score: 3

GCTGAGTACAATGCCATTTCATATACCCAACAAATGAGGTTGAGGACAGCAGTTGAACTTTTGAAGGCTACAAAGGACATAGAATCCCAGTTGGAGAAGgtcagtgttg ... tacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGACCCCCATGTCAGCGAATTCCTGTACGAGAAAGCTAGCACAAAAGACAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatcacttcttttgaaaaatagttacaaatgcgaaaccctctttacttgacagATTTGTTCCCCATTGCTGATTCTCCACGGAGCAGCAGACTTGGTTACCGACCCCCATGTCAGCGAATTCCTGTACGAGAAAGCTAGCACAAAAGACAAGA
                                      ccctctttactt  CT-rich tract
           ttttgaaaaatagtta  TA-rich tract