Sequence
atgc intronic sequence ATGC exonic sequencegtaattgacaatgttataatgttgaaaagtctcctagaatcaaatcgcatgttagcgtatctggagggaatcattatctagtttaattgaacaatattcattatcctgttgatcaattacttattatatttttcgttcttgtcattttgctttttttcattattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAGTTTGAGGAAAT
Basic information
species | Physcomitrella patens |
transcript | PP1S9_238V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 7
gtaattgacaatgttataatgttgaaaagtctcctagaatcaaatcgcatgttagcgtatctggagggaatcattatctagtttaattgaacaatattcattatcctgttgatcaattacttattatatttttcgttcttgtcattttgctttttttcattattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAGTTTGAGGAAAT
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-----------------------------------------atatgccattgtgcc--atctgcagctg-ttatcctatagttt--ttgtgctactgctgttgtc---ttgaccaa--acataccttact----ggagctggctttttgctcc--------------agGCCATTGCTGGAGAAGCTGGCGTACCATTCTTTTACCGAGCAGGTTCTGAATTTGAGGAAAT
upper sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 7
gtaattgacaatgttataatgttgaaaagtctcctagaatcaaatcgcatgttagcgtatctggagggaatcattatctagtttaattgaacaatattcattatcctgttgatcaattacttattatatttttcgttcttgtcattttgctttttttcattattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAGTTTGAGGAAAT
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-----------------------------------------------------------------ggacgccattgtgccatct--ccagctgttatcctatagttt-ttgtgctattgct-gttgtcttgaccaaacataccttactggagctgtctttttgccccagGCCATTGCTGGAGAAGCTGGTGTACCATTCTTTTACCGAGCAGGCTCTGAATTTGAGGAAATMapped 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|162195893|gb|FC375626.1|FC375626EST: GTGTTCTTCTGACTGGTCCACCTGGCACTGGAAAGACTCTGCTGGCCAAG GCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAG
genomic: GTGTTCTTCTGACTGGTCCACCTGGCACTGGAAAGACTCTGCTGGCCAAGgtaattgaca ... ttattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAG
EST:
gi|162202061|gb|FC377267.1|FC377267EST: GTGTTCTTCTGACTGGTCCACCTGGCACTGGAAAGACTCTGCTGGCCAAG GCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAG
genomic: GTGTTCTTCTGACTGGTCCACCTGGCACTGGAAAGACTCTGCTGGCCAAGgtaattgaca ... ttattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAG
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:
28 (upstream exon),
23 (downstream exon)
Score:
6GGTGTTCTTCTGACTGGTCCACCTGGCACTGGAAAGACTCTGCTGGCCAAGgtaattgaca ... ttattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAGTTTGAGGAAAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattacttattatatttttcgttcttgtcattttgctttttttcattattggtagGCCATTGCTGGAGAAGCCGGGGTTCCATTCTTCTACCGCGCAGGGTCTGAGTTTGAGGAAAT
ttttgctttttttcat CT-rich tract
attttgctttttttca TA-rich tract