Sequence
atgc intronic sequence ATGC exonic sequence...ccaaacggggccttacttgccgtaattactctagtgggcattgcagtataactatcatcgatgcaacatctaaactctttcgtacttgtatttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCCCAAGGCCATGCCCTTCAGTTCACCATCGCTCCAGACTCCCCCGCCACTC
Basic information
species | Oryza sativa |
transcript | LOC_Os11g38800.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g38800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G303431_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------------ccaaacggggccttacttgccgtaattactctagtgggcattgcagtataactatcatcgatgcaacatctaaactctttcgtacttgtatttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCCCAAGGCCATGCCCTTCAGTTCACCATCGCTCCAGACTCCCCCGCCACTC
||| | || || | | ||| || | | | | | | |||| | | ||| || ||| | ||| || | |||||||| ||||||| | || || ||||||||||| |||||||| || || ||| |||| ||||| ||||| ||||||||||||||||||||||||| |
gtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatct-gtcgatgatatggcacaccatccatctaagt--tctctgtgcttcttc-ttcttcctttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCCAGGGGCCGCGCCCTCCAGTTTGCCATCGCTCCAGACTCCCCCGCCACCCMapped 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|163927687|gb|EG710503.1|EG710503EST: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
EST:
gi|88199974|gb|CI199824.1|CI199824EST: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACTAAGACAG GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
EST:
gi|87033485|gb|CI188109.1|CI188109EST: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAG GAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
genomic: ATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCC
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:
75 (upstream exon),
74 (downstream exon)
Score:
8CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttctaa ... tttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCCCAAGGCCATGCCCTTCAGTTCACCATCGCTCCAGACTCCCCCGCCACTC
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtataactatcatcgatgcaacatctaaactctttcgtacttgtatttttggcagGAAGCGGCTGCAATTGCTGCAGCAGAGGTGGCATTCATCCTGCAATCAGCCCAAGGCCATGCCCTTCAGTTCACCATCGCTCCAGACTCCCCCGCCACTC
atctaaa putative branch site (score: 8)
tattttt putative PPT
ttgtattttt TA-rich tract