Sequence
atgc intronic sequence ATGC exonic sequenceCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
Basic information
species | Physcomitrella patens |
transcript | PP1S167_51V6.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatc-tcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
| |||||||| |||||||||||||| || || ||||| ||||| |||||||||||||||||||| | | ||| ||||||||||| || |||||| || ||| | || || |||| || | |||| ||| | ||| | | | | | | || | | || || | |||
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctc----ttgttcttagctacat-----------atgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattgcag------------------------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
|| |||||||| ||||| || || || || || ||||| |||||||||||||| ||||||||||| | ||||| |||||||| || ||||||||| | || | ||| | | || ||||| | | | | | | || ||| ||| | || | || | || | | | |
CTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAGgtatc----tgcttgttctcattatgagttac---caatgcc-gctaactattattttatttggaactactatatgttaactctccttgtggtgccttca--actgcag---------------------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
|| |||||||| || ||||| ||||| || |||||||||||||| || ||||||||||||||||| | ||||| ||||||||||| || |||||| | | ||| | ||| || || || | | | |||| | ||||| |||| ||| | || | | | |
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatt---tctttcatcc--attattgactgtacgtgtcattttaaagaaatcctctctattaacacttccattttctggtg----tcttcaaactgcag------------------------------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgt-attggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
||||||||| | ||||| || || || |||||||| ||||| ||||||||||| ||||| ||||| |||| || ||||||||||| ||||||| | || | |||||| ||| | ||||| | | |||| ||| | ||| ||| || | | ||
CTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAGgtctctgataca--aacttaatc---tgcggt--tcaatcgccgttggaat-tgtttatcctgcatcttacgattttgtttcacttgttgacag-------------------------------------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgt-attggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
||||| ||| | ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||| |||| | ||||||||||| ||||||| | || | |||||| | | |||| | | | | | || ||| | ||| ||| || | | ||
CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAGgtctctgataca--aacttaatccgtgg-----ttcagt-tgtcgttggaattgtttatcctgcatcttacgattttgtttcactttttgacag-------------------------------------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
|| |||||| | ||||| || || || ||||||||||| ||||| |||||||| ||||| ||||| | || ||||| |||||||||||||||| | | | | |||| || | |||| | | | | ||| |||| |||| || || | | | || | || || | | ||| || | | | |
CTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAGgtgtgatttat----gcttgatccataattatagtga-----tcaataaaatcctggg--ccaaga--tgccttcgcctgaatatttgatgtaatgtggtt--tttttcatgtgattgcag---------------------------
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag-
| || ||| | ||||| || || || ||||| ||||||||||| |||||||| ||||| ||||| | || || ||||||||||| ||||||||| ||| | | || ||| | | | | | | || || | ||| | | || | || || | | || || || |||||| || | | |||| |
TTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAGgtatgccttttttaaattt--ttgcagaaccttccttttttttcccccttcttctttccttttaggttgtcattaag-gttggaagggatctggttgttgaaac--cctttggaatgtgcaatactaatact-gtttccatggtcccag
upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 11
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag
| |||||| | ||||| || || || ||||| || || |||||||||||||| ||||| ||||| |||||||| || || ||||| ||||||| || ||| | || || | | || ||| | | | | | | | || | || | ||| || | || |
TTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAGgt-ccgttttttaaattttctttatccaccat------tgtttcttgaaccctct----accatgagtactaacataaaattgatgtgatcccag-----------------------------------------------------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|37827186|gb|BJ585198.1|BJ585198EST: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG CAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
genomic: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatt ... cttggtacagCAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
EST:
gi|37836637|gb|BJ594645.1|BJ594645EST: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG CAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
genomic: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatt ... cttggtacagCAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
EST:
gi|162181126|gb|FC357285.1|FC357285EST: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG CAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
genomic: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatt ... cttggtacagCAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
EST:
gi|162164628|gb|FC341923.1|FC341923EST: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG CAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
genomic: GAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatt ... cttggtacagCAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAAC
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:
18CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatt ... cttggtacagCAACTTGTTCCGGGTGTTTGGGGCCGCTACCGGAAGTGAGGAAGCGTCAACCTTGGAAGCTAGCAAGACTCCAAACAG
<
<
<