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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_Os08g32630.1
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|29670150|gb|CB666425.1|CB666425
EST:     CCCAATTGTGCGACAG                         ATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
genomic: CCCAATTGTGCGACAGgtattcctga ... cttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGT
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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctgtcacttggcatccttagtgcacatagtcacgtacagttgctgacccttccagatttcacattttaaaatacaactcttctgtccttatccaagATCCGGTCAGGCAGAAAACCAGATGGAGTATGCCTTGTTGTTGGTACTTGTGCTCGTGGATTTGACAGAAATACAACAAGTGACATTATTTTCAGTAGCT

- - ctgtcac
- - - - - - -ggcatcc
- - - - - - - - - - - - -gcacata
- - - - - - - - - - - - - - - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - - - - - - - - -ccttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatacaa