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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaagcttatttctcggcttgtttttatcctccttctattaatactactattactaaaaaaaatgaactttctgtgtcttcacatgtagtgttaagtggtctcggcgttcacagtttactgatctctgaatcatagttacagttagaaacgaatattcagagttttagaattatcacgatgtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGCCCTGGTGCTAGTCCGTTTGGAGCACCTGGTGGCAATCCATTTGCTGGCA

Basic information

species Physcomitrella patens
transcript PP1S110_13V6.1
intron # 4
splice site 3'
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|162166028|gb|FC340424.1|FC340424
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
EST: gi|100451985|gb|CJ975042.1|CJ975042
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
EST: gi|208352398|gb|DC906181.1|DC906181
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGANCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
EST: gi|100429860|gb|BY978125.1|BY978125
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGGCA-CAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGG
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATG-CAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGG
EST: gi|100440859|gb|BY962347.1|BY962347
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTC
EST: gi|100442213|gb|BY963106.1|BY963106
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAA
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAA
EST: gi|208357241|gb|DC910652.1|DC910652
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
EST: gi|162176403|gb|FC353588.1|FC353588
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
EST: gi|162184458|gb|FC359204.1|FC359204
EST:     CTCTTTTGGTGCTAACAGCGTGAAG                         AGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC
genomic: CTCTTTTGGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGC

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: 16 (upstream exon), 35 (downstream exon)
Score: 4

GGTGCTAACAGCGTGAAGgtcaagctta ... gtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGCCCTGGTGCTAGTCCGTTTGGAGCACCTGGTGGCAATCCATTTGCTGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacagttagaaacgaatattcagagttttagaattatcacgatgtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGCCCTGGTGCTAGTCCGTTTGGAGCACCTGGTGGCAATCCATTTGCTGGCA
                         agttttagaattat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaagcttatttctcggcttgtttttatcctccttctattaatactactattactaaaaaaaatgaactttctgtgtcttcacatgtagtgttaagtggtctcggcgttcacagtttactgatctctgaatcatagttacagttagaaacgaatattcagagttttagaattatcacgatgtttgtgcagAGATACGCAATGCAACAGATGTTGAAGTCAATGAGCGGGGGCGCTGGGGGCCCTGGTGCTAGTCCGTTTGGAGCACCTGGTGGCAATCCATTTGCTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG