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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCCATGTCGGACGACGAGATGAAGGAGGAGAAGGAGCTCGATCTGACTTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtacccgcgctgctgattttgctgcagagtttggattactttagggtttaagggaattggagttttggagttgtggtgattcgtgttcactggcat...

Basic information

species Physcomitrella patens
transcript PP1S119_137V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 2
---GTCGCCATGTCGGACGACGAGATGAAGGAGGAGAAGGAGCTCGATCTGACTTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtacccgcgctgctgattttgctgcagagtttggattactttagggtttaagggaattggagttttggagttgtggtgattcgtgttcactggcat-------------------------------------------------------------
   ||  ||||||||||||| ||||     |||||||||||| | ||||| |||||||| || || ||||||||||||||  ||||||| ||| |||  ||||||  ||     | || || |||||     | | | |  ||   |||  |||||  || |  | | |||    | || || ||  |  |  | | |||  |                                                             
GAGGTTACCATGTCGGACGATGAGA---GAGAGGAGAAGGAGTTGGATCTCACTTCTCCGGAAGTTGTCACCAAGTACAAGAGCGCCGCGGAGATTGTTAACAgtgtgt---tacact-ctcattttttgttaaattcttaatgggtttttggtttttggtacattgggttcattactt-tgatgggttattgttaatgggttatttgcgtttttatttttcttatgttgatgagttatgttttgttttgttttaattaaacag

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 5'ss of exon 1
---GTCGCCATGTCGGACGACGAGATGAAGGAGGAGAAGGAGCTCGATCTGACTTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtacccgcgctgctgattttgctgcagagtttggattactttagggtttaagggaattg-gagttttggagttgtggtgat-tcgtgttcactggcat-
   |   | |||||||| ||||| |     |||||||||||| | ||||| |||||||| || || |||||||| |||||  |||| |||||| |||| ||||||   |||   |  |  |  | |   |  | | ||    || ||     |  ||      ||| || ||||    || |||||   |   |||   | |  | 
CTCGAAACGATGTCGGATGACGAAA---GAGAGGAGAAGGAGTTGGATCTCACTTCTCCTGAAGTCGTCACCAAATACAAGAGCGCTGCTGAGATTGCTAACAgt---tactttctttcttcgtatatatatatatttgttttttctgatatgcatatatatgttgcgatttttttttttttggtggggtttcgttggtttgggtt
















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|67569798|gb|BJ942622.1|BJ942622
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|208397136|gb|DC908150.1|DC908150
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|100439250|gb|BY980169.1|BY980169
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|100384797|gb|BY950787.1|BY950787
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|162183958|gb|FC359328.1|FC359328
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|100445208|gb|BY982837.1|BY982837
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|67719527|gb|BJ969786.1|BJ969786
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|162161202|gb|FC337265.1|FC337265
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|100397823|gb|BY990419.1|BY990419
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|67716276|gb|BJ966536.1|BJ966536
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
EST: gi|18365978|gb|BJ198056.1|BJ198056
EST:     TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACA                         AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG
genomic: TTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCG

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: 19

GTCGCCATGTCGGACGACGAGATGAAGGAGGAGAAGGAGCTCGATCTGACTTCTCCCGATGTGGTCACCAAGTACAAATGCGCCGCTGAGGTTGCCAACAgtaagtaccc ... ttgtttacagAGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA




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