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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttaaggtttgacacagaatttgggtttgaagacacagccttggaaaagcttatagattattcctttttttcgcttaaaaaaataaactgcacttttcggtttagctcataatcagctcaagaattaatttcatcttgtttttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAATCTTACACTGCAGTTAAGAAGGATTATATCGTTTCTGTCACCAGAAACT

Basic information

species Oryza sativa
transcript LOC_Os04g52640.3
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52640.3 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G031536_T01 (Zea mays), 3'ss of exon 2
gtaggttaaggtttgacacagaatttgggtttgaagacacagccttggaaaagcttatagattattcctttttttcgcttaaaaaaataaactgcacttttcggtttagctcataatcagctcaaga------attaatttcatcttgtttttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAATCTTACACTGCAGTTAAGAAGGATTATATCGTTTCTGTCACCAGAAACT
                                                                    ||   | |  || |    |  | || || ||| || ||||||| || | | | | | ||      |||  |||  |||||| ||| |  |||||||| |||||||||||| |||||||||| | ||||| |||||| || |||||||||||||| ||| ||||| | ||||| ||| ||||||| |||||||
-------------------------------------------------------------------gttgggtactgttgagctgactacctacattttgcgttttagcttatgagctggttatgactttgtattgtttttgtcttgtgtttagcacagGGTGAGCGTAAGGAGAAGAACTTTGACATAATGAAGGCAGCAGGGGGAAAATCTTACACTGCTGTTGAGAAGCAGTATATTGTTCCTGTCACTAGAAACT

upper sequence: LOC_Os04g52640.3 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 13
gtaggttaaggtttgacacagaatttgggtttgaagacacagccttggaaaagcttatagattattcctttttttcgcttaaaaaaataaactgcacttttcggttt-agctcataatcagctcaagaatta-----atttcatcttgtttttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAATCTTACACTGCAGTTAAGAAGGATTATATCGTTTCTGTCACCAGAAACT
                                                                    ||  ||    || |    || | || || |||  ||||| |||| || | | | | || | ||      ||||  |||||| || ||  ||||| || |||||||||||| |||||||||| | ||||| | |||| || |||||||||||||| ||  ||||| | ||||| ||| ||||||| |||||||
-------------------------------------------------------------------gttggttcttgttgatctgatcacctacattttggggtttgagcttatgagctggttaatattttgtattattttttcttgtgttcggcacagGGCGAGCGTAAGGAGAAGAACTTTGACATAAGGAAGGCATCAGGGGGGAAATCTTACACTGCTGTCGAGAAGCAGTATATTGTTCCTGTCACTAGAAACT
















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|29632157|gb|CB637166.1|CB637166
EST:     CAGAGTCTTGGAAAAGCCGAGGGAGAAGGGTTTTCGATATATATGTACAG                         GGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAA
genomic: CAGAGTCTTGGAAAAGCCGAGGGAGAAGGGTTTTCGATATATATGTACAGgtaggttaag ... tttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAA
EST: gi|29633874|gb|CB638883.1|CB638883
EST:     CAGAGTCTTGGAAAAGCCGAGGGAGAAGGGTTTTCGATATATATGTACAG                         GGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAA
genomic: CAGAGTCTTGGAAAAGCCGAGGGAGAAGGGTTTTCGATATATATGTACAGgtaggttaag ... tttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggtttagctcataatcagctcaagaattaatttcatcttgtttttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAATCTTACACTGCAGTTAAGAAGGATTATATCGTTTCTGTCACCAGAAACT
                           aattaat  putative branch site (score: 3)
                                 tttcatcttgttttt  CT-rich tract
                           aattaatttcatcttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttaaggtttgacacagaatttgggtttgaagacacagccttggaaaagcttatagattattcctttttttcgcttaaaaaaataaactgcacttttcggtttagctcataatcagctcaagaattaatttcatcttgtttttggtgcagGGTGAACGTAAGGAGAAGGACTTTGACATCAAGAAGGAAGCAGGTGGTAAATCTTACACTGCAGTTAAGAAGGATTATATCGTTTCTGTCACCAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG