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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcatctcactcacatcgatgagtatcctccattcgctttgaccttctctttcattcacacctggtttgagactcaaggctacgcaaatggatctttttgttgctgtgcgcgggctttgcgtaccaccaccatgctgcaaaacttaccgctgacaaactcttaaagcacttaatctactttcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGGGTAGCCCGTAGTTACACGTCTCTTGTGGCTCCATTTTATGTCTTTCCGT

Basic information

species Physcomitrella patens
transcript PP1S396_8V6.1
intron # 22
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|162179346|gb|FC356295.1|FC356295
EST:     CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
genomic: CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
EST: gi|162185897|gb|FC360997.1|FC360997
EST:     CACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
genomic: CACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
EST: gi|100402314|gb|BY954774.1|BY954774
EST:     CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAGGGAGCAGCAGGG
genomic: CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
EST: gi|162185898|gb|FC360998.1|FC360998
EST:     CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
genomic: CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
EST: gi|162177303|gb|FC353460.1|FC353460
EST:     CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
genomic: CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
EST: gi|37836632|gb|BJ594640.1|BJ594640
EST:     CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAG                         GTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG
genomic: CTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGG

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

AGATATGAATGATGCCACTCATGGAGCTGAGAATATCAGAAGTGATATCACTGCACTGTCACAGCGCTATGCTGTTGTGAAACGTGATGAAACATGCAAGgttaatcatc ... tcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGGGTAGCCCGTAGTTACACGTCTCTTGTGGCTCCATTTTATGTCTTTCCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaacttaccgctgacaaactcttaaagcacttaatctactttcttgtacagGTTTGTGGACAGCGGATATTGGCATCAAAAGGAGCACAAGGAGCAGCAGGGGTAGCCCGTAGTTACACGTCTCTTGTGGCTCCATTTTATGTCTTTCCGT
                                      tctactttctt  CT-rich tract
                                  ttaatcta  TA-rich tract