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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcaccatctccttcagcctccgtttcttgattctatcttgcttttgagtttttaccagattgctgatccgttctttttgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT

Basic information

species Oryza sativa
transcript LOC_Os07g38530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 1
--------------gtacggcaccatctccttcagcctccgtttcttgattctatcttgcttttgagttttta--ccagattgctg-atccgttctttttgct--gtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
               |||  |   | || || |  || |||||  ||||  |  |||        |     |   ||   |  ||| |||  | ||  ||| |    ||||| || |||||||||||||||||||||||||||||  ||
gtatggaatcgccgctaccactgtagctactcctaccaccgttgtttgaccc-gtctgctcaccaatccgctgatccgtttccctgcatctttcctccttgtttaacgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT

upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G034779_T01 (Zea mays), 3'ss of exon 1
-----------------gtacggcaccatctccttcagcctccgtttcttgattctatcttgcttttgagttttta--ccagattgctgatccgttctttttgctgt---gcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
                   || | | |  |||||   ||  |||| | ||||  |  |||        |     |   ||   |  |||   | ||| | || || |   ||||| || |||||||||||||||||||||||||||||  ||
gtatggaatcgccgctaccactggagctcctcctatggcg-ccgtcttttgaccc-gtctgctcaacaatcccctgatccgtttccctgcatctttcctctttctttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
















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|58652513|gb|CK041193.1|CK041193
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|88394443|gb|CI605784.1|CI605784
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|58658300|gb|CK046980.1|CK046980
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|29629432|gb|CB634441.1|CB634441
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|29622036|gb|CB627047.1|CB627047
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|88583784|gb|CI701291.1|CI701291
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|29629006|gb|CB634017.1|CB634017
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
EST: gi|88423128|gb|CI613429.1|CI613429
EST:     GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGG                         TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
genomic: GCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT

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: 55 (upstream exon), 49 (downstream exon)
Score: 7

GGTGAGAGGAGCTAGAATGATGGGCCCCAAGGCCAACGCCGCCGCCGCCGGCGACCTCCCGGAGTACGCCGAGGTCGATCCCACCGGCCGGTACGGACGGgtacggcacc ... tgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcttgcttttgagtttttaccagattgctgatccgttctttttgctgtgcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
                            tgctgat  putative branch site (score: 7)
                                  tccgttctttttgct  CT-rich tract
              agttttta  TA-rich tract