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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgattcctgaaaccgggaaaggcttccagggggtttcggtgtacaatttagctacttcaacataatttcattttccaatagtttatttttattttatttggtttactggttccatgtgtagacctttttgtaggttgacgtttttgtgtatttcgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC

Basic information

species Physcomitrella patens
transcript PP1S17_208V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_208V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ30223 (Selaginella moellendorffii), 3'ss of exon 6
gtattgattcctgaaaccgggaaaggcttccagggggtttcggtgtacaatttagctacttcaacataatttcattttccaatagtttatttttattttatttggtttactggttccatgtgtagacctttttgtaggttgacgtttttgtgtatttcgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC
                                                                                                  |||     | ||| | |  |  | | |  ||| |      |  ||||     ||| |      |  |||| ||||| ||||||||||||||||| || ||||||||  ||||||| || ||||||||||| |  || |   | || ||    ||||| ||||| |||||
-------------------------------------------------------------------------------------------------gtatgcaaatcacttggtgtagctcttgggcttctc-----taaacgt----atgtctcctctctttcagGCCAATTCAAGGCTATCAACGATGAAGGGATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC

upper sequence: PP1S17_208V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 6
gtattgattcctgaaaccgggaaaggcttccagggggtttcggtgtacaatttagctacttcaacataatttcattttccaatagtttatttttattttatttggtttactggttccat-gtgtagacctttttgtaggttgacgtttttgtgtatttcgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC
                                                                                                        || | |   |  | | |||||| |  |   |    |  |    | ||| |  |    ||  |||| ||||| ||||||||||||||||| || ||||||||  ||||||| || ||||||||||| |  || |   | || ||    ||||| ||||| |||||
--------------------------------------------------------------------------------------------------------gtatgcaaatcacttagtgtag-ctctcaggcttctctaaacgtatgtctcctctcttt--cagGCCAATTCAAGGCTATCAACGATGAAGGAATGCCTCACCACCAGAGACCCTTCATGAAGGGAACCCTGTACATCCACTTCTCGGTCGACTTCCCCGAGTC
















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|162277167|gb|FC453389.1|FC453389
EST:     TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|162268923|gb|FC446031.1|FC446031
EST:     TTGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|162178563|gb|FC355015.1|FC355015
EST:     TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|67569046|gb|BJ941870.1|BJ941870
EST:     TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|162277166|gb|FC453388.1|FC453388
EST:     TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|162268924|gb|FC446032.1|FC446032
EST:     TTGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
EST: gi|208373963|gb|DC944696.1|DC944696
EST:     TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAG                         GTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT
genomic: TGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTT

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: 29 (upstream exon), 12 (downstream exon)
Score: 6

AGCTTGACAGAGGCTCTATGTGGTTTCCGATTTCCTTTGGTTCACTTGGATGGAAGACAGCTTCTAATTAAGTCTGATGCTGGGGAGATCATCAAGCCAGgtattgattc ... cgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccatgtgtagacctttttgtaggttgacgtttttgtgtatttcgattgacagGTCAATTTAAGGCTATCAACGATGAGGGTATGCCTCATTACCAGAGGCCTTTCATGAAGGGCAGGCTATTTTTGCATTTTAACGTCGAGTTCCCTGAGTC
                        ggttgac  putative branch site (score: 6)
                tttttgta  TA-rich tract