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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggattgggtggtgcaggggatggggatgggcttgtgatgcttagcagttccggcgggaccgtagcccggtgcccaggggttggtagcggggagg...

Basic information

species Physcomitrella patens
transcript PP1S341_23V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S341_23V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g11970.1 (Oryza sativa), 5'ss of exon 1
TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggattgggtggtgcaggggatggggatgggcttgtgatgcttagcagttccggcgggaccgt-----agcccggtgcccaggggttggtagcggggagg-
| |||||||||||||| ||||| || || ||||| |||||| | |||||||| || ||||| || |||||||| || ||||| || || | |||||| |||| | |    | | |    ||     ||    |  || | |  ||||   |  ||||  |   |   |     |  | | |   | |  | ||||   |    |  
TAAGCATCCACATAGGGCAGGCGGGCATCCAGGTGGGGAATTCTTGCTGGGAACTATACTGCCTCGAGCATGGCATCCAGCCGGACGGCCTCATGCCCAGgttctt---ctcgat--cccaattcttgctcgtctgcatctcttgct-gtcttttcctacttaattttgtgaaattctgatattcggatgatggttttgtcctgtt
















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|18324871|gb|BJ156866.1|BJ156866
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162167933|gb|FC344871.1|FC344871
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18358529|gb|BJ190588.1|BJ190588
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|100420027|gb|BY975938.1|BY975938
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18331875|gb|BJ163887.1|BJ163887
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162153183|gb|FC329589.1|FC329589
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162197748|gb|FC374998.1|FC374998
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162229157|gb|FC404516.1|FC404516
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162186501|gb|FC363265.1|FC363265
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162159253|gb|FC335106.1|FC335106
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162174343|gb|FC350414.1|FC350414
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18353132|gb|BJ185187.1|BJ185187
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18366573|gb|BJ198652.1|BJ198652
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162162283|gb|FC338065.1|FC338065
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162195647|gb|FC370310.1|FC370310
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA

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: 31 (upstream exon), 35 (downstream exon)
Score: 68

TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGAGACGGGGGCGGGGAAGCACGTCCCGCGCGCCGTGTTCGTGGATCTGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggattgggtggtgcaggggatggggatgggcttgtgatgcttagcagttccggcgggaccgtagcccggtgcccaggggttggtagcggggagg

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