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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacacagcaaaatccaccgagataatgccattcaatcgtttgattccgtgccactttctccttttttttctttctcaacccaatgtaaaatctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAGGGCGGCATCATCGACTCCGATGGCGAGGTGATCGCGAGAGGGGATGGAT

Basic information

species Oryza sativa
transcript LOC_Os07g37580.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37580.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057475_T01 (Zea mays), 3'ss of exon 8
-cacacagcaaaatccaccgagataatgccattcaatcgtttgattccgtgccactttctccttttttttctttctcaacccaatgtaaaatctc------tgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAGGGCGGCATCATCGACTCCGATGGCGAGGTGATCGCGAGAGGGGATGGAT
             |   ||  ||  ||||  |  | |||     | || ||  | ||    | |       |  |      |  ||   ||           | |||||||||||  || |||| ||||||||  |||| |||||||||| |||||||||||| ||||||||||| || || |||||| ||||||| || || || |
gtggttgcttctttagtccatgaccatgcgttgtactcgccctgt-ccatg--aattctgtcatcaaagcataacgaggtgcgctgggcaactctgacgaacggcagGTGAAGGCGATCCGGATCGAGCCGGGCCTGCGCGTGGGCAGCAGCACCAAGGGCGGTATCATCGACTCGGACGGGGAGGTGCTCGCGAGGGGCGACGGGT
















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|86497705|gb|CI140338.1|CI140338
EST:     AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAG                         GTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACACA-
genomic: AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAGgtactgtgtt ... tctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCAC-CAA
EST: gi|88963956|gb|CI032873.1|CI032873
EST:     AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAG                         GTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
genomic: AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAGgtactgtgtt ... tctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
EST: gi|86831221|gb|CI297490.1|CI297490
EST:     AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAG                         GTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
genomic: AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAGgtactgtgtt ... tctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
EST: gi|86416146|gb|CI030157.1|CI030157
EST:     TGAAGGATGGCAGCTATGTCATATCCCCCTATGTGGAGTACTTCAAG                         GTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
genomic: TGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAGgtactgtgtt ... tctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
EST: gi|86907346|gb|CI296450.1|CI296450
EST:     AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAG                         GTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG
genomic: AGATGAAGGATGGCAGCTATGTCAAATCCCCCTATGTGGAGTACTTCAAGgtactgtgtt ... tctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgccactttctccttttttttctttctcaacccaatgtaaaatctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAGGGCGGCATCATCGACTCCGATGGCGAGGTGATCGCGAGAGGGGATGGAT
                                             tctct  CT-rich tract
                ttttttttctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacacagcaaaatccaccgagataatgccattcaatcgtttgattccgtgccactttctccttttttttctttctcaacccaatgtaaaatctctgacagGTGAAGGCTCTCAGGATTGAGCCGGGAATGCGGGTGGGCAGCACCACCAAGGGCGGCATCATCGACTCCGATGGCGAGGTGATCGCGAGAGGGGATGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA