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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctgtcacttggcatccttagtgcacatagtcacgtacagttgctgacccttccagatttcacattttaaaatacaactcttctgtccttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGTGCTCGTGGATTTGACAGAAATACAACAAGTGACATTATTTTCAGTAGCT

Basic information

species Oryza sativa
transcript LOC_Os08g32630.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G851815_T02 (Zea mays), 3'ss of exon 7
ttatctgtcacttggcatccttagtgcacatagtca-cgtacagttgctgacccttccagatttcacatttta---aaatacaactcttctgtccttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGTGCTCGTGGATTTGACAGAAATACAACAAGTGACATTATTTTCAGTAGCT
  |||||  | |||      |||||    |||  || | ||| |||||   |  |||| |||| ||  |   |   |  ||| |||||||||||||| | |||||||||||| || ||||||||||||||| | ||||||||||||||| |||| |||| |||||| || | ||||||||||||||| ||||||||||||||||
-aatctg--atttgcttctattagta-gtatatccatcttaccgttgcaaccatttcctgattccatctacaagttagttacgactcttctgtccttgtgcaagATCCGGTCTGGTAGAAAACCAGATGGAATGTGCCTTGTTGTTGGTGCTTGCGCTCATGGATTCGAAAAAAATACAACAAGTGATATTATTTTCAGTAGCT

upper sequence: LOC_Os08g32630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 3'ss of exon 7
ttatctgtcacttggcatccttagtgcacatagtcacgtacagttgctgacccttccagatttcacattttaaaatacaactcttctgtcct---tatccaa--gATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGTGCTCGTGGATTTGACAGAAATACAACAAGTGACATTATTTTCAGTAGCT
   | |   | |    |   ||||  || | | |  | |||  |||   |     |  |  | |||||  |   | ||   |  |   |      ||||  |  |||  ||   || || || ||||||||||| ||||||||||||||| ||||||| ||||| |||   |  ||  ||||||||||  | || | |||||| |
-gctttactaatc--tagtgttagatcaaagattatcctac--ttgggaaataagcatgtctacacatggtccgaaaccgtttgttaatgtaaaatatcttacagATGAGGGGTGGAAGGAAGCCAGATGGAGTTTGCCTTGTTGTTGGTTCTTGTGCACGTGGTTTTACAAATAACTCAACAAGTGATGTCATATACAGTAGTT
















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|29676352|gb|CB672627.1|CB672627
EST:     GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAG                         ATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
genomic: GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAGgtattcctga ... cttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
EST: gi|300215548|gb|HO088174.1|HO088174
EST:     GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAG                         ATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
genomic: GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAGgtattcctga ... cttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
EST: gi|58656158|gb|CK044838.1|CK044838
EST:     GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAG                         ATCCGGTCAGGCAGAAAACCGAGATGGAGTATGCCTTGTTGTTGGTACTTG
genomic: GTCGACTTGTTATTGATGCTATGGGTAATTTTTCCCCAATTGTGCGACAGgtattcctga ... cttatccaagATCCGGTCAGGCAGAAAACC-AGATGGAGTATGCCTTGTTGTTGGTACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgacccttccagatttcacattttaaaatacaactcttctgtccttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGTGCTCGTGGATTTGACAGAAATACAACAAGTGACATTATTTTCAGTAGCT
 tgctgac  putative branch site (score: 2)
                                   ctcttctgtccttatc  putative PPT
              atttcacattttaaaa  TA-rich tract