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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTACAAGTCCCGGCAAGAATTTGCCGAATTTTACAAGAGTGCTCTCCTGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtaccttcatcatcctttgcaaaattcatgttcatatcttctcttctcttttcattcgcgcatactgcgtcactggtcatcaattggcatattcat...

Basic information

species Physcomitrella patens
transcript PP1S131_74V6.1
intron # 2
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|162251835|gb|FC426943.1|FC426943
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|22133353|gb|BQ827693.1|BQ827693
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|208374842|gb|DC956115.1|DC956115
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|162243863|gb|FC423180.1|FC423180
EST:     GAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: GAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|208344424|gb|DC916761.1|DC916761
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|162230348|gb|FC406912.1|FC406912
EST:     GAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCCTTGTTGGGGAACAATATTTA
genomic: GAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGG-CCTTGTTGGGGAACAATATTTA
EST: gi|162243433|gb|FC425129.1|FC425129
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|208359725|gb|DC946601.1|DC946601
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|162243434|gb|FC425130.1|FC425130
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|208392191|gb|DC957270.1|DC957270
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
EST: gi|208357810|gb|DC918600.1|DC918600
EST:     TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTG                         GATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT
genomic: TGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTAT

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: 19 (upstream exon), 30 (downstream exon)
Score: 3

GTATTACAAGTCCCGGCAAGAATTTGCCGAATTTTACAAGAGTGCTCTCCTGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtacct ... ttgagtgcagGATCTAGCATTTGATCTATCACTGGCGGCCTTGTTGGGGAACAATATTTATAATTTCGGAGAGCTTCTTGCTCATCCCATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTACAAGTCCCGGCAAGAATTTGCCGAATTTTACAAGAGTGCTCTCCTGTACTTGGCTTACACCTCTGTGGAAACATTGTCGGAAGACTTCAAGCTGgtttgtaccttcatcatcctttgcaaaattcatgttcatatcttctcttctcttttcattcgcgcatactgcgtcactggtcatcaattggcatattcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG