Sequence
atgc intronic sequence ATGC exonic sequenceCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcatttaatagatttagatacgtgttctagtcattgttgttctgaccatccagtatgtcttagcattgttggattttcatt...
Basic information
species | Physcomitrella patens |
transcript | PP1S10_201V6.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 13
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcatttaatagatttagatacgtgttctagtca--ttgttgttctgaccatccagtatgtcttagcattgttggattttcatt----
|| || ||||| ||||| |||||||| |||||||||||||||||||| || || |||||| | |||||||| || | | ||||| || ||| | || || | || |||| |||||| | | || || || ||| | || | || || | | | || || || | ||| || |
ATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGACTGgtgagaattt------tatttcagtaatagttgttcatcagtcttttagaaagatttcttttttgtgcttaaaatacagattttattttgtaactttacaatatga
upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 13
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgtt---cttataccatattcatttaatagatttagatacgtgttctagtcattgttgttctgaccatccagtatgtcttagcattgttggatt-ttcatt------------------------------------------------------------------------
|| || ||||| || || |||||||| |||||||||||||||||||| || || |||||| | |||||||| || | | ||||| || ||| |||| || | |||| | | | | |||| || || | | || | || | | ||| | | | | | ||| | | || || ||
ATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGGCTGgtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttact--ttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacag
upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 13
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcatttaatagatttagatacgtgttctagtcattgttgttctgaccatc-cagtatgtcttagcattgttggattttcatt----
| || || || || || |||||||| || ||||| ||||||||||| |||||||| || || |||||||| || | ||||||||||| ||| |||| ||| |||||| | | | ||| || || | | |||||| | |||| || | || |||| | | | | || | ||| ||
AATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaa--tcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatag
upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 13
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcattta-atagatttagatacgtgttctagtcattgttgttctgaccatccagtatgtcttagcattgttggattttcatt--
| || || |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| ||||||||||| | ||||||| || ||| |||| ||| || ||| | | | || ||| | || | | || ||| ||| || | | | || ||||| | | ||| | |
TATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtccttct-cagttttagcttatgtggaagtttctgttgattttagaaattacc-ttttaatgcttca-tatgtgatgggggaaagccttttaaagttt
upper sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcatt-taatagatttagatacgtgttctagtcattgttgttctgaccatccagtatgtctt-agcattgttggattttcatt
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AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttatttt-attttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa-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|100448629|gb|CJ972928.1|CJ972928EST: ACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTT GCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTA
genomic: ACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttctt ... ggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTA
EST:
gi|162165021|gb|FC342212.1|FC342212EST: ACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTT GCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTA
genomic: ACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttctt ... ggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTA
EST:
gi|208375011|gb|DC956407.1|DC956407EST: TCCGGAAGGCCTN NCTGAGATGCCTGCTGACAGTGGTTATNCCAGCTTACCTTGCTGCAAGAT
genomic: TCCGGAAGG-CTTgtatgttctt ... ggggcttcagGCTGAGATGCCTGCTGACAGTGGTTAT-CCAGCTTACCTTGCTGCAAGAT
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:
34 (upstream exon),
33 (downstream exon)
Score:
18CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttctt ... ggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCCGGGAAAGTGAAGTGTCTGGGAAGCCCGA
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