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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGAGCTCCCTTTCCGCTCCCCCAGTAACGAGTTGCGCTGCGTTGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcattgcttctcatcgctctggaaggcgttctgatgtcttgttgatttttgtctcaattttgcactactcggtttctgatttggactctactgtc...

Basic information

species Physcomitrella patens
transcript PP1S6_198V6.1
intron # 1
splice site 5'
intron type U2

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|67709844|gb|BJ965660.1|BJ965660
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|7582814|gb|AW699031.1|AW699031
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162248096|gb|FC420101.1|FC420101
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|18369053|gb|BJ201138.1|BJ201138
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAANAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|7147838|gb|AW509760.1|AW509760
EST:     GCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: GCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162250013|gb|FC427114.1|FC427114
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162209881|gb|FC386023.1|FC386023
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|37847272|gb|BJ605280.1|BJ605280
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162202561|gb|FC379244.1|FC379244
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTTTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162245704|gb|FC419604.1|FC419604
EST:     GAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: GAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|15729018|gb|BI741095.1|BI741095
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|18327147|gb|BJ159148.1|BJ159148
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|18369077|gb|BJ201162.1|BJ201162
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162253005|gb|FC429066.1|FC429066
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|18366870|gb|BJ198950.1|BJ198950
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162202562|gb|FC379245.1|FC379245
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162213753|gb|FC390368.1|FC390368
EST:     ATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTTTGCCCTGGAAAGGCATGCAAG
genomic: ATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|15327299|gb|BI487887.1|BI487887
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162253004|gb|FC429065.1|FC429065
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|18335425|gb|BJ167444.1|BJ167444
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162203006|gb|FC380078.1|FC380078
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|67572978|gb|BJ945802.1|BJ945802
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162245986|gb|FC421875.1|FC421875
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162209880|gb|FC386022.1|FC386022
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162211965|gb|FC388045.1|FC388045
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|7047264|gb|AW477158.1|AW477158
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|67703412|gb|BJ963645.1|BJ963645
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|6102360|gb|AW126830.1|AW126830
EST:     GCAACCGGAGCTCTTGAAACGCGGCCACCATG                         GTGAATGTTCCTAAGACGAACAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: GCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|67723922|gb|BJ974181.1|BJ974181
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162213754|gb|FC390369.1|FC390369
EST:     ATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: ATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|37850368|gb|BJ608376.1|BJ608376
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|67696359|gb|BJ956592.1|BJ956592
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
EST: gi|162203414|gb|FC378822.1|FC378822
EST:     TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATG                         GTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG
genomic: TGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAG

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: 94

CGAAGAGCTCCCTTTCCGCTCCCCCAGTAACGAGTTGCGCTGCGTTGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcatt ... cgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGAGCTCCCTTTCCGCTCCCCCAGTAACGAGTTGCGCTGCGTTGCGCTCCATTGAATTTTGCAACCGGAGCTCTTGAAACGCGGTCACCATGgtaattcattgcttctcatcgctctggaaggcgttctgatgtcttgttgatttttgtctcaattttgcactactcggtttctgatttggactctactgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT