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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataattcagtttctctacagcagttttggtttttgaatatgccgtactcaaccgaaaccgtgatttgttgttgatttgtggacgtctccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG

Basic information

species Physcomitrella patens
transcript PP1S54_95V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_95V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0080g00860.t01 (Vitis vinifera), 3'ss of exon 2
gtgataattcagtttctctacagcagttttggtttttga-atatgccgtactcaaccgaaaccgtgatttgttgttgattt-gtggacgt-ctccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
                      | | ||||  || || |  | |    ||   ||    ||   | ||   || |  ||||  || |  |  |  ||| ||||   || ||||| |||||||||||||| ||||||||||| ||||  ||||
----------------------gtatttttttttcttcatgtttttattatataatttgaaattttatgaattttccattttatgaatttgttttgtttcagGAACACTCAGCCCCGGTTCCAGTTCATTGTGATGAATCGGCGCAACACAG
















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|208359918|gb|DC934891.1|DC934891
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
EST: gi|100445401|gb|BY983030.1|BY983030
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
EST: gi|208352362|gb|DC902007.1|DC902007
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
EST: gi|208390427|gb|DC933684.1|DC933684
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
EST: gi|100389800|gb|BY971152.1|BY971152
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
EST: gi|100412769|gb|BY974898.1|BY974898
EST:     AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAG                         GCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
genomic: AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG

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), 27 (downstream exon)
Score: 17

AGTCGCAAGGATGTGGAGGGTTCACTCTTTGTTGTAAAAAGgtgataattc ... tccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtactcaaccgaaaccgtgatttgttgttgatttgtggacgtctccgttgcagGCGGACACAGCCGCGGTTCCAGTTCATAGTGATGAATCGTCGCAGTACAG
                           tgttgat  putative branch site (score: 17)
                                           tctccgtt  putative PPT
                     atttgtt  TA-rich tract