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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattctatcactaaagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 8
gtaaattc-tatcacta-aagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC
|||||||| ||  | ||  | | | ||  ||||||| ||| ||  ||||||| | ||| |  | |||||||||||||||||||||||||||||| ||||| |||||||||||||||  ||||||||| |||||||| || ||
gtaaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G540538_T01 (Zea mays), 3'ss of exon 8
gtaaattc-tatcacta-aagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC
|||||||| ||| |  |  | ||| |||||||||||  ||||   ||||||| |   | || | |||||||||||||||||||||||||||||| ||||| || |||||||| |||||||||||||| |||||||| || ||
gtaaattcatattataatgaaagtaccctttgaagttctttt---agtttgattggtcatgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGATGCCCAAGAGAAGGTCCTCCC

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 8
gtaaattc-tatcacta-aagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC
|||||||| ||| |  |  | ||| |||||||||||  ||||   ||||||| |   | || | |||||||||||||||||||||||||||||| ||||| || |||||||| ||||                         
gtaaattcatattataatgaaagtaccctttgaagttctttt---agtttgattggtcatgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC-------------------------

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 8
-gtaaattctatcactaaagagttccctt---tgaagtgg---tttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC
  |||||   || |  |||  | | | ||   | || |||   ||| |   | || | |     |  ||| | ||| | |||   |||||||| ||||| || |||||||||||||||||| | ||||  |||||||| | ||| ||
gttaaatatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttat-tcctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGATGTACAGGAGAAAGCTCTACC

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|38482919|gb|CF966721.1|CF966721
EST:     CCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAAGAGAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGA
genomic: CCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACA-AGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGA
EST: gi|89167316|gb|CI252847.1|CI252847
EST:     AGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: AGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|27576661|gb|CA999355.1|CA999355
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCT
EST: gi|300215864|gb|HO088490.1|HO088490
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|38470488|gb|CF954619.1|CF954619
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|89199046|gb|CI253120.1|CI253120
EST:     AGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCGGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: AGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|30227286|gb|CB965178.1|CB965178
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|88694901|gb|CI738939.1|CI738939
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTC
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTC
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
EST: gi|2311475|gb|C27630.1|C27630
EST:     NCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGGATGAACCTCTCTTCACCCTTTATCTGTGAGTTTT-CCGTGA
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTG-ATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGA
EST: gi|88729190|gb|CI752700.1|CI752700
EST:     CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG                         GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT
genomic: CCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGAT

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: 68 (upstream exon), 75 (downstream exon)
Score: 108

TGGAGAAAGCAAAATACATCTACATTGCTGGCTTTTTCCTTACGGTCTCCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattcta ... ttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC
                                  gactaac  putative branch site (score: 108)
                                             ttgttttc  putative PPT
                      tttttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattctatcactaaagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA