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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggtctttaggaatatatggttgattcatcagtttagagttgttgagacatgcgcttatcattcttttgttgagcacacatgttaaccactccaaaatgccttttgtacttgaacggatccttacggagttgcacttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 14
gtaatggtctttaggaat-----atatggttgattcatcagtttagagttgttgagacatgcgcttatcattcttttgttgagcacacatgttaaccactccaaaatgccttttgtacttgaacggatccttacggagtt---gcacttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
||||||||  |   | |       |||  |||| ||||||||  | || |||  ||| ||      ||||    |            ||  |||| |  ||         ||| |  ||| ||   ||  | | | | ||   ||| |||||||||||| ||||| || |  ||||||||||||||||| ||||| ||||||||||
gtaatggttgtgttgtactcagggtatcattgaatcatcagta-atagctgtgaagaaataaatggatcaactgt------------cacattaagctttctg-------tttgggtcttcaatccattgtcatgcaattagggcatttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
















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|163920010|gb|EG709816.1|EG709816
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|33803665|gb|CF327708.1|CF327708
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|86251819|gb|CI019011.1|CI019011
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29615419|gb|CB620431.1|CB620431
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|2798032|gb|AA751326.1|AA751326
EST:     AGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|58694158|gb|CK082845.1|CK082845
EST:     AAAGAAAATGAG                         GGTTCATCAAGCCATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29646292|gb|CB651299.1|CB651299
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|5002870|gb|AU067979.1|AU067979
EST:     GTTTGGATT-AAAGCCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: GTTTGGATTAAAAG-CACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29674106|gb|CB670381.1|CB670381
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29679501|gb|CB675776.1|CB675776
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|58686515|gb|CK075202.1|CK075202
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29667425|gb|CB663700.1|CB663700
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|66916241|gb|CX103089.1|CX103089
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|58676643|gb|CK065330.1|CK065330
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|88831197|gb|CI082007.1|CI082007
EST:     AGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29615344|gb|CB620356.1|CB620356
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
EST: gi|29689096|gb|CB685371.1|CB685371
EST:     AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG                         GGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
genomic: AGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 69 (downstream exon)
Score: 29

ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtct ... ttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaaatgccttttgtacttgaacggatccttacggagttgcacttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG
                            tccttac  putative branch site (score: 29)
                                            cttcatttc  putative PPT
           ttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggtctttaggaatatatggttgattcatcagtttagagttgttgagacatgcgcttatcattcttttgttgagcacacatgttaaccactccaaaatgccttttgtacttgaacggatccttacggagttgcacttcatttcagGGTTCATCAAGCAATGCTGGGGAATCATCCAGCATGGATATTGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA