Sequence
atgc intronic sequence ATGC exonic sequenceTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactgacacttactttcgatcagcttccttggccttggtctccagtttactgtttattattcgactcgaagttacccttcgtgattatttgaata...
Basic information
species | Physcomitrella patens |
transcript | PP1S47_46V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactgacacttactttcgatcagcttccttggccttggtctcc-agtttactgtttattattc-gactcgaagttacccttcgtgattatttgaata------
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AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtttagatcccaattatgcatatgaggtcaaagagataaatgtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G03230.1 (Glycine max), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgta---------ttcactgacacttactttcgatcagcttccttggccttggtctccagtttac-tgtttatta--ttcgactcgaagttacccttcgtgattatttgaata-----------------------------------------------------------------------
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TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTACCTCTGATGAATCCTGAGCTCTTTCTTCGAGTTGGAATTAAACCTCCAAAGgtgatttaccctttcactgctctttctagtctctgacttctattagtgttaatctatgttttagatttttagtagctttgttatgacatttttcctacatatttttttagtggaagcttacttgtaatggctgtacttttgaattttacacttgatcaaaatcttttcaattctaattttcag
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G03180.1 (Glycine max), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgta---------ttcactgacacttactttcgatcagcttccttggccttggtctccagtttactgtttattattcgactcg--aagttacccttcgtgattatttgaata--------------------------------------------------------------------------
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TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTGCCTCTAATGAATCCTGAGCTCTTCCTTCGAGTTGGAATTAAACCTCCAAAGgtgatttacctttttactgctctttctagtctctgatttctattagtgttaatctatgtttta--gatttttagtagctttgttatgtcattttttctacatatttttttagtggaagcttatttgtaatggccgtacttttgaattttacatttaatcaaaatcttttcaattctaattttcag
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgt-attcac---------tgacacttacttt--------cgatcagcttccttggccttggtctccagtttactgtttattattcgactcgaagttacccttcgtgattatttgaata--------------------------
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GGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAATCAATTGAGCTACCTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcatactttaatttgttagttattctgtatggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttt-tccttaattaaaaagtctcttaaattttatttttttgcagMapped 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|208398538|gb|DC912383.1|DC912383EST: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAG GGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAA-CTCTTTTAGCACGA
genomic: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA
EST:
gi|100405000|gb|BY991388.1|BY991388EST: TTAATGAATCCTGAAACTCTT-CTGCGAGTTGGCATAAAAC-TCCCAAAG G-TGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACG
genomic: TTAATGAATCCTGAA-CTCTTTCTGCGAGTTGGCATTAAACCTCC-AAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACG
EST:
gi|162269527|gb|FC445083.1|FC445083EST: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAG GGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA
genomic: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA
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:
16 (upstream exon),
33 (downstream exon)
Score:
5TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
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