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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGGGAGAGATTGAAAGCCCCGCGGGCGTCAGTGCACCTTGTGCCAACCCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtctgtgccttaatttggtacattcgtaacatatgctctttttttgtttcaatttgctcgccattgtactgtcggaatgtgagtgataccaatttgtgggtggtcgctgtgatagtctgtgtcggattgaggtgggttttttcgtggcgaatgatggtttagattaatttgcag

Basic information

species Physcomitrella patens
transcript PP1S3_96V6.2
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|18362646|gb|BJ194717.1|BJ194717
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162160001|gb|FC335663.1|FC335663
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162215136|gb|FC390761.1|FC390761
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|18345057|gb|BJ177098.1|BJ177098
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|18327061|gb|BJ159062.1|BJ159062
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162196438|gb|FC375430.1|FC375430
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162197017|gb|FC375229.1|FC375229
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162155745|gb|FC331774.1|FC331774
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|100416688|gb|BY993038.1|BY993038
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCAGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162269780|gb|FC444933.1|FC444933
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162193872|gb|FC368734.1|FC368734
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|18364484|gb|BJ196557.1|BJ196557
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|18366915|gb|BJ198995.1|BJ198995
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|67570059|gb|BJ942883.1|BJ942883
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
EST: gi|162265474|gb|FC440800.1|FC440800
EST:     CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGG                         AGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG
genomic: CCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAG

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), 32 (downstream exon)
Score: 8

GCCGGGGAGAGATTGAAAGCCCCGCGGGCGTCAGTGCACCTTGTGCCAACCCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtct ... taatttgcagAGCCTTTGCTGGTGAGGGCGGCTAGGCGGGAGAAAGTAGAGCGTGCCCCAGCATGGATGATGAGGCAGGCGGGCCGGTACATGGCTGTGTATCGAAAGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGGGAGAGATTGAAAGCCCCGCGGGCGTCAGTGCACCTTGTGCCAACCCGGCGCGAAGCATTGCATTGTGTGGCTGAGTCGGTGGAGAGACATGTGGgtgggtgtctgtgccttaatttggtacattcgtaacatatgctctttttttgtttcaatttgctcgccattgtactgtcggaatgtgagtgataccaatttgtgggtggtcgctgtgatagtctgtgtcggattgaggtgggttttttcgtggcgaatgatggtttagattaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA