Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcgctgtatctgattgtttatagtagtttttggaacatgctcaagctcaacttttatggttttggcgcatagtcagacatctcaacacttaatgaatatgattgcgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
Basic information
species | Physcomitrella patens |
transcript | PP1S126_38V6.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
--gtaaagcgctgtatctgattgtt--tatagtagtttttggaacat-gctcaagctc-----aacttttatggttttggcgcatagtcagaca---tctcaacactt----aatgaatatgattgcgggttt----cagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
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gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC
upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
--------gtaaagcgctgtatctg-attgtttatagtagtttttggaacatgctcaagctcaacttttatggttttggcgcatagtca-gacatctcaacacttaa-tgaatatgattgcgggttt----cagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
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ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttcta-ttctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-
upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaaagcgctgtatctgattgtttatagtagtttttggaacatgctcaagctcaacttttatggttttggcgcatagtcagacatctcaacacttaatgaatatgattgcgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
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--------------------------------gtttgcattgcacacgaat--aattctt----ctttaaatgatctccaactcgcataacacgttct---catacttgtgt-tcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGGMapped 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|162260419|gb|FC435045.1|FC435045EST: TGCTGGAACAGTCTCCATTTGTTGAGAAGTTGTTGAAGAAGGGCTACGAG GTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACT
genomic: TGCTGGAACAGTCTCCATTTGTTGAGAAGTTGTTGAAGAAGGGCTACGAGgtaaagcgct ... cgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACT
EST:
gi|162196001|gb|FC372692.1|FC372692EST: TGCTGGAACAGTCTCCATTTGTTGAGAAGTTGTTGAAGAAGGGCTACGAG GTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACT
genomic: TGCTGGAACAGTCTCCATTTGTTGAGAAGTTGTTGAAGAAGGGCTACGAGgtaaagcgct ... cgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACT
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),
22 (downstream exon)
Score:
3GAAACCAGGACAGAAGCAAATTTACTATCTCACTGGTCAAGATAGGAAACTGCTGGAACAGTCTCCATTTGTTGAGAAGTTGTTGAAGAAGGGCTACGAGgtaaagcgct ... cgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggcgcatagtcagacatctcaacacttaatgaatatgattgcgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC
acttaat putative branch site (score: 3)
ttaatgaatatgatt TA-rich tract