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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT

Basic information

species Oryza sativa
transcript LOC_Os01g74580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 5
gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT
                                         |  | || |   ||| |  ||  |||  |  || | | |      |  |||| |  | |   ||      | |||  |  ||||||||||||||||||||||| |||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||||||| |||||||||| ||||||
----------------------------------------gtaatctg-gaaagcatatgcatgtgc--ttatacacacacaaaaaaattttagac-tatacccaa-----ataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT

upper sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 4
gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT
                       ||||    ||   | |   |  |||      ||   |        ||| ||  |    || |   ||   | |  |   | ||   |  ||||         ||||||| || || ||||| || ||||||||||| ||||||   |||||||||||||| |||||||| ||||||||| | |||||||| ||||| |||
-----------------------gtttatttaacaacttatcttgttgaaatctcatg-attctcattgtaataattg---gtccctactactattgctcacatagacttttcaat---------ttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
















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|218478483|gb|FG953980.1|FG953980
EST:     CTTCGTGGCCGAGCATATTACTACCTTGCTGATCATGATGTTGCATCCAG                         GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
genomic: CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAGgtaaagcgta ... aattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
EST: gi|58597523|gb|CK008051.1|CK008051
EST:     CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAG                         GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
genomic: CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAGgtaaagcgta ... aattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
EST: gi|29616879|gb|CB621891.1|CB621891
EST:     CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAG                         GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
genomic: CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAGgtaaagcgta ... aattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
EST: gi|58681128|gb|CK069815.1|CK069815
EST:     CTTCGTGGCCGAGCATATTACTACCTTGCTGATCATGATGTTGCATCCAG                         GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
genomic: CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAGgtaaagcgta ... aattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
EST: gi|29679525|gb|CB675800.1|CB675800
EST:     CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAG                         GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA
genomic: CTTCGTGGCCGAGCATATTACTACCTCGCTGATCATGATGTTGCATCCAGgtaaagcgta ... aattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT
                                         tattaat  putative branch site (score: 2)
                                     acaatattaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG