Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaacggcttacatttgaaacatgggcatgaaatctatacaaccatttcgttgatgttgaatgctttaaggttttcgaacgtgataaagctatccaccaccttagcgaggtttttatctaatttaaggtttcttgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAAAGGATATGGTTTCTGTGTATATCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S58_254V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S58_254V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv00s0561g00030.t01 (Vitis vinifera), 3'ss of exon 10
gtaaggaacggcttacatttgaaacatgggcatgaaatctatacaaccatttcgttgatgttgaatgctttaaggttttcgaacgtgataaagctatccaccaccttagcgaggtttttatctaatttaaggtttcttgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAAAGGATATGGTTTCTGTGTATATCAG
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----------------------------------aaatctcatcgacatctctggagccaccagaagttata---tttcc--atgtcaggcagctgtcgtatattc-----atattctaat--aatatact-tttgacccattacagGCCCTTGCGTGGTTTTGATCTTGTTAAGGATAGAGACACAGGAAACTCTAAGGGATATGGTTTCTGTGTTTATCAGMapped 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|162183241|gb|FC360391.1|FC360391EST: CCTTATTATTTGACAGAGATTCAAATTAAGGAGTTGCTCGAGTCTTTTGG GCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAA
genomic: CCTTATTATTTGACAGAGATTCAAATTAAGGAGTTGCTCGAGTCTTTTGGgtaaggaacg ... tgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAA
EST:
gi|162184034|gb|FC359404.1|FC359404EST: CCTTATTATTTGACAGAGATTCAAATTAAGGAGTTGCTCGAGTCTTTTGG GCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAA
genomic: CCTTATTATTTGACAGAGATTCAAATTAAGGAGTTGCTCGAGTCTTTTGGgtaaggaacg ... tgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAA
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),
33 (downstream exon)
Score:
10ATGCCGCTGGAGGTGCGGATGGACCTGATCGGATCTTTGTTGGAGGCTTGCCTTATTATTTGACAGAGATTCAAATTAAGGAGTTGCTCGAGTCTTTTGGgtaaggaacg ... tgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAAAGGATATGGTTTCTGTGTATATCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatccaccaccttagcgaggtttttatctaatttaaggtttcttgaactccagGCCTTTGCGAGGTTTTGATCTTGTCAAAGACCGGGACACAGGCAACTCTAAAGGATATGGTTTCTGTGTATATCAG
atctaat putative branch site (score: 10)
tttctt putative PPT
tttttatctaatttaa TA-rich tract