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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC

Basic information

species Physcomitrella patens
transcript PP1S61_267V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ14300 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtca-tctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC
| | || || ||| ||| || | | | | | | || | || | || || |||||||||||| | ||| ||||| || |||||||| ||| || ||||| | |||||||||||||||||||||| || || || || || ||||| || ||
-------------------------------------------------------------------------------------------------gtaagccag--tgatttcgcgtccttttgtgaaata----cgggtgggaatcagcaagaatcgatccaatccagGGCCTCCGGGTTCTGGCAAGGGCACGCAATCGCCGATTATCGAGGAGAATTACTGCCTGTGCCATTTGGCCACTGGTGATATTCTCCGGGCAGCCGTGGC

upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ24129 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC
| || | || || | |||| ||| | || | || | ||| | || |||||| ||||||||||| ||||| || ||||| ||||| ||||||||| |||| ||| |||| || ||||||| ||||| ||||| || || || || ||
------------------------------------------------------------------------------------------------------gtaatctcccttctctttcatgttc---cttg-gagaaatcctcgcagtgagctcttgctttctc-agGGCCGCCGGGATGTGGCAAGGGCACACAATCTCCCATCCTCAAGGAGCAGCATTGCTTGTGTCACCTGGCCACTGGCGATATGCTCCGGGCCGCCGTGGC

upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18155 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtca-tctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC
| | || || ||| ||| || | | | | | | || | || | || || |||||||||||| | ||| ||||| || |||||||| ||| || ||||| | |||||||||||||||||||||| || || ||||| || ||||| || ||
-------------------------------------------------------------------------------------------------gtaagccag--tgatttcgcgtccttttgtgaaata----cgggtgggaatcagcaagaatcgatccaatccagGGCCTCCGGGTTCTGGCAAGGGCACGCAATCGCCGATTATCGAGGAGAATTACTGCCTGTGCCATTTGGCCACTGGTGATATGCTCCGGGCAGCCGTGGC

upper sequence: PP1S61_267V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ35190 (Selaginella moellendorffii), 3'ss of exon 1
gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC
| || | || || | |||| ||| | || | || | ||| | || |||||| ||||||||||| ||||| || ||||| ||||| ||||||||| |||| ||| |||| || |||||||| ||||| ||||| || || || || ||
------------------------------------------------------------------------------------------------------gtaatctcccttctctttcatgttc---cttg-gagaaatcctcgcagtgagctcttgctttctc-agGGCCGCCGGGATGTGGCAAGGGCACACAATCTCCCATCCTCAAGGAGCAGCATTGCTTGTGTCACTTGGCCACTGGCGATATGCTCCGGGCCGCCGTGGC

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|208384519|gb|DC914991.1|DC914991
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|18368471|gb|BJ200556.1|BJ200556
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|18369302|gb|BJ201388.1|BJ201388
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|208363576|gb|DC939767.1|DC939767
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|208357429|gb|DC910742.1|DC910742
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGTCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|162152018|gb|FC328439.1|FC328439
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|18375207|gb|BJ206785.1|BJ206785
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|162258566|gb|FC434781.1|FC434781
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
EST: gi|100431663|gb|BY960311.1|BY960311
EST:     GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTG                         GGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC
genomic: GCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGC

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: 34 (upstream exon), 33 (downstream exon)
Score: 6

GCTGCTAATCTGGAGGATGTGCCCAACGATGTGCTCTTCCATGAGCTTCTGCGCCGCATGAAGTGTGCCCCCAAACAGGAGAAGCGCCTCATCCTTGTTGgtatatgcac ... tgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC
                    gtttgat  putative branch site (score: 6)
 ttattgttttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcacgcttttgggtttcaggtgttttgagatttctgggttgcaaaacgtagaatgcctagcgagcattttctaaccgtggttgttacatttgaatgctgatttggtttttcgtatttgtttagttttgtgtttgattgttattgttttgtattgtgtcatctagGGCCTCCGGGATGTGGGAAGGGAACCCAATCGCCCATTCTCAAGGAGGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC