Sequence
atgc intronic sequence ATGC exonic sequenceAGATGGATTGGGAGCAGAGATTGTGGGAACGTTCGTGTTGGTCTACACTGTGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttcacttattcacggtggtacatttcaattacagggaaagttggagggtggatgtgttttatcactgatttaatcagatctgaattgctgctgacgacgacataaaaaaataaaaataaaaataaaaaaaactgaaacaaaaaaaataaaaactcttcgtcttgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S102_107V6.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 1
AGATGGATTGGGAGCAGAGATTGTGGGAACGTTCGTGTTGGTCTACACTGTGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttcacttattcacggtggtacatttcaattacagggaaagttggagggtggatg-tgttttatcactgatttaatcagatctgaattgctgctgacgacgacataaaaaaataaaaataaaaataaaaaaaactgaaacaaaaaaaataaaaactcttcgtcttgcag
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CGACGGCCTCGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCACGTTCCGgttagtat-accaact---actactgcagtaaagattcagaga---tggaagtatttttactgttttctgagtgattgatttttgttttaatttgcgcgatcttccacag----------------------------------------------------------------
upper sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G174807_T01 (Zea mays), 5'ss of exon 2
AGATGGATTGGGAGCAGAGATTGTGGGAACGTTCGTGTTGGTCTACACTGTGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttcacttattcacggtggtacatttcaattacagggaaagttggagggtggatgtgttttatcactgatttaatcagatctgaattgctgctgacgacgacataaaaaaataaaaataaaaataaaaaaaactgaaacaaaaaaaataaaaactcttcgtcttgcag
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CGACGGCCTAGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCATGTGCCGgtgagtacagtatcagccttgccttcctgcttattcgcctcgtccgtccgtg--caagctcgacttatcgatggtttctttgtggacgaatgaacag----------------------------------------------------------------------------
upper sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 5'ss of exon 2
AGATGGATTGGGAGCAGAGATTGTGGGAACGTTCGTGTTGGTCTACACTGTGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttcacttattcacggtggtacatttc---aattacagggaaagttggagggtggatgtgttttatcactgatttaatcagatctgaattgctgctgacgacgacataaaaaaataaaaataaaaataaaaaaaactgaaacaaaaaaaataaaaactcttcgtcttgcag
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AGATGGGCTTGGTGCTGAGATTGTTGGCACCTTCGTCCTTGTCTACACTGTCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaatt----attgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaag-------------------------------------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|161982343|gb|EE296257.1|EE296257EST: TGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCG GTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGT
genomic: TGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttca ... cgtcttgcagGTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGT
EST:
gi|100411113|gb|BY956329.1|BY956329EST: TGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCG GTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGTACATTTGGCC
genomic: TGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttca ... cgtcttgcagGTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGTACATTTGGCC
EST:
gi|100446499|gb|CJ970798.1|CJ970798EST: TGTTCTCCGCCACCGACGCCNAGCGCAGCGCTCGTGACTCTCATGTGCCG GTGCTTGCCCCTCTTCCTATTGGATNCGCAGTGTTTCTGGTACATTTGGCC
genomic: TGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttca ... cgtcttgcagGTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGTACATTTGGCC
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:
35 (upstream exon),
35 (downstream exon)
Score:
284AGATGGATTGGGAGCAGAGATTGTGGGAACGTTCGTGTTGGTCTACACTGTGTTCTCCGCCACCGACGCCAAGCGCAGCGCTCGTGACTCTCATGTGCCGgtatgtttca ... cgtcttgcagGTGCTTGCCCCTCTTCCTATTGGATTCGCAGTGTTTCTGGTACATTTGGCCACCATTCCCATCACCGGAACTGGCATTAACCCTGCACGTAGTCTGGGCG
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