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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attacttggaactcaattatctaaagagcatttccagtagaacaaaactaaaaggaaaacgtgttgctaccttgtttactaagattaagcatccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGATGGACCTGATGACTGCTCTGCAGCTTGTGATGAAGAAGTCAAGCGCTCAT

Basic information

species Oryza sativa
transcript LOC_Os07g12650.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12650.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G132929_T03 (Zea mays), 3'ss of exon 1
attacttggaactcaat-tatc-taaagagcatttccagtagaacaaaac-taaaaggaaaacgtgttgctaccttgtttactaagattaagcatccatgcagGGA---AGAGACTCCAGTTGAGGCCC---CACCTGCCCCGGTTCTTGGAGAGCCGATGGACCTGATGACTGCTCTGCAGCTTGTGATGAAGAAGTCAAGCGCTCAT
   | | |  | ||| | |||  | ||    ||     || || |   || |      || ||  |  |||     ||| || | ||||  |       |||||||    |||||   || || ||      ||||| ||||||||||||| || |||||||||||||||||||| |||||||| || |||||||||||| |       
---attagcgattcactgtattatgaattcgatcgtttgttgaccgctacatgcctacaacacaggaagctcatcagttcacgatgattttgtgctttggcagGGATCAGGAGACCGTAGCTGTGGTTGAGGCACCTACCCCGGTTCTTGGGGAACCGATGGACCTGATGACTGCCCTGCAGCTCGTCATGAAGAAGTCAGGT------
















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|55432687|gb|CV729364.1|CV729364
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCA-GAGAC-TGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|88722319|gb|CI745829.1|CI745829
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|13806613|gb|AU181586.1|AU181586
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|88358899|gb|CI619403.1|CI619403
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|88357562|gb|CI623616.1|CI623616
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCC
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCC
EST: gi|568095|gb|D38930.1|D38930
EST:     CGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: CGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|88332492|gb|CI651652.1|CI651652
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGCTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|88339791|gb|CI649048.1|CI649048
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|58586800|gb|CF985108.1|CF985108
EST:     GTCGCTGTCGG-CCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|218485304|gb|FG956287.1|FG956287
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
EST: gi|427734|gb|D23869.1|D23869
EST:     GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC                         GGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT
genomic: GTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGCgtaagtttcc ... atccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactaaaaggaaaacgtgttgctaccttgtttactaagattaagcatccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGATGGACCTGATGACTGCTCTGCAGCTTGTGATGAAGAAGTCAAGCGCTCAT
 aactaaa  putative branch site (score: 2)
                             tttactaagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attacttggaactcaattatctaaagagcatttccagtagaacaaaactaaaaggaaaacgtgttgctaccttgtttactaagattaagcatccatgcagGGAAGAGACTCCAGTTGAGGCCCCACCTGCCCCGGTTCTTGGAGAGCCGATGGACCTGATGACTGCTCTGCAGCTTGTGATGAAGAAGTCAAGCGCTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT