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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaatcaatccccttcgatttctccgatttctcctctcctcctcctagagagagcattattataggtagatcgagaaggaaccagctgacggatcgatgatttggttccgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAGAACGTGGCCGCCGATGCCGCCCCCAAGTACCGCGGCCTCCTCGGCACCG

Basic information

species Oryza sativa
transcript LOC_Os11g48040.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G000510_T04 (Zea mays), 3'ss of exon 1
gtatccaatcaatccccttcgatttctccgatttctcctctcctcctcctagagagagcattattataggtagatcgagaagg--aaccagctgacggatcgatgatttggttc--cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAGAACGTGGCCGCCGATGCCGCCCCCAAGTACCGCGGCCTCCTCGGCACCG-
                         ||||  || ||   | ||    || | |||||| |     || |   ||||  |  |   | ||           |  | ||||| | |  |    ||||| | || || ||||| || || ||||||||||| ||||| ||||||||||||||||| | |||||  |||||| ||  | || || ||  |  ||   ||  
-------------------------ctccttttccttgccgccgagaccca-agagagaagggggatggcaggatcacgccgcccatcccatcctatcccctttaatttgctgcatcttctcgcagATATGTACCATCCCGCTCGACACGGCCAAGGTCAGGCTCCAGCTGCAGAAGAACGTCGTCGCCGCCGCCGCCTCCGGGGAC-GCCGCGCCAGCGCTTCCCA
















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|88745668|gb|CI769028.1|CI769028
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88296156|gb|CI667546.1|CI667546
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88345333|gb|CI655991.1|CI655991
EST:     CCTTCGCCGGCCGCTTCACCGNAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGNCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|117251481|gb|CT844185.1|CT844185
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88695949|gb|CI739524.1|CI739524
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88345950|gb|CI632423.1|CI632423
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGNAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88573462|gb|CI665033.1|CI665033
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88729445|gb|CI752955.1|CI752955
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGCATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88307967|gb|CI646402.1|CI646402
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88332650|gb|CI660168.1|CI660168
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88695493|gb|CI737531.1|CI737531
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88432647|gb|CI690486.1|CI690486
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88719972|gb|CI745271.1|CI745271
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88589532|gb|CI705420.1|CI705420
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88587690|gb|CI704394.1|CI704394
EST:     CCTTCGCCGGCCGGTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88573786|gb|CI665555.1|CI665555
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|58661525|gb|CK050205.1|CK050205
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|58594298|gb|CF992606.1|CF992606
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88342270|gb|CI658925.1|CI658925
EST:     CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
EST: gi|88333370|gb|CI642407.1|CI642407
EST:     CCTTCGCCGGCCGCTTCANCGCAAGCGCCATCGCTGCATGCTTCGCTGAG                         GTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG
genomic: CCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAG

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: 72 (upstream exon), 60 (downstream exon)
Score: 16

CGCAAACGCCGCCGCCGGTATGCCGGAGCACGGGTCGAAGCCCGACATCTCCTTCGCCGGCCGCTTCACCGCAAGCGCCATCGCTGCATGCTTCGCTGAGgtatccaatc ... cgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAGAACGTGGCCGCCGATGCCGCCCCCAAGTACCGCGGCCTCCTCGGCACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtagatcgagaaggaaccagctgacggatcgatgatttggttccgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAGAACGTGGCCGCCGATGCCGCCCCCAAGTACCGCGGCCTCCTCGGCACCG
                    agctgac  putative branch site (score: 16)
                                 atgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaatcaatccccttcgatttctccgatttctcctctcctcctcctagagagagcattattataggtagatcgagaaggaaccagctgacggatcgatgatttggttccgatccgcagGTGTGCACGATCCCCCTGGATACGGCCAAGGTGAGGCTTCAGCTGCAGAAGAACGTGGCCGCCGATGCCGCCCCCAAGTACCGCGGCCTCCTCGGCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC