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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgttgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagtttactgagtcagatctgtctgcgtgataatgacttcaaattgttacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT

Basic information

species Physcomitrella patens
transcript PP1S85_75V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 14
gtacctgttgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagtttactgagtcagatctgtctgcgtgataatgacttcaaattgttacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT
                         | |   |  | ||| |  |||   |    ||||| ||  |   | |   ||| |   | || | |  |  | | || |     || |      |  |||||| |||| |||||||| ||||||||||||||||||||||| ||  | |||||  | ||||| || ||  |||| |||||||| || ||||| ||||||||| 
------------------------gtaaccctcatgcatgacctgacatt----gttattcttaaactccttaattattt--taagttttaacctcctaatcaactgatctatgaaaaaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGAGCATATGACACACGCAACATCTTCCAGTCGCTTGACCTCGCCTGGTCAC

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
gtacctgttgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagttta--ctgagtcagatctgtctgcgtgataatgacttcaaattgttacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT
                                                ||||||  | | ||    | |  ||| ||       || | | | |     | |  |    ||  |  || | |   |||| | ||||| |||||| | || ||||||||| |||||||||| || || ||  |||||||||||||  |||| ||||||||||| ||||| || ||| |  
----------------------------------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgca-aacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 14
gtacctgt-tgcttcatattttctgtttatgatatttcatcatttgatgctctctgttatcctgtagagcttagtt--tactgagtcagatctgtctgcgtgataatgacttcaaattgt-tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT
||| || | |   ||     | || | | |   |  |     |||| |  |     |  | || |||   | | ||   |  || | | |||     |  | |   ||   |    |||| ||     ||| | ||||| |||||||| ||||| |||||| |||| ||||| || |||||  |||||||||||||  |||| ||||||||||| ||  | || ||| |||
gtatctctctttctctctcctcctttctgtagaaactatgtgtttgttttttcacatctttctctagcaataatttctcatagattaaaatcacaaagtattaacctggggttgggttgtctaaaattcagCTTTATCTGGAGTTCCTAGACAAATTCGAGAGGAAATTTGTGGCTCAAGGGGCTTATGATACCCGCAACATCTTCCAGTCACTAGATTTGGCGTGGACAT

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|37827904|gb|BJ585916.1|BJ585916
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|208370179|gb|DC944404.1|DC944404
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|37844176|gb|BJ602184.1|BJ602184
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|162274940|gb|FC450591.1|FC450591
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|162274941|gb|FC450592.1|FC450592
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|208345114|gb|DC925440.1|DC925440
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|37848050|gb|BJ606058.1|BJ606058
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|67698442|gb|BJ958675.1|BJ958675
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|162190699|gb|FC367585.1|FC367585
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|37833609|gb|BJ591621.1|BJ591621
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
EST: gi|18337987|gb|BJ170011.1|BJ170011
EST:     AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG                         TTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT
genomic: AAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGT

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: 33 (upstream exon), 35 (downstream exon)
Score: 23

TTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTGgtacctgttg ... tacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactgagtcagatctgtctgcgtgataatgacttcaaattgttacttgacagTTGTATCTCGAGTTCCTTGACAAGTTCGAGCGGAAGTTTGTCGCCCAAGGTCCTTATGATACCCGTGACATTTTCCAGTCACTGGACCTTGCCTGGTCAT
                                      aaattgtta  TA-rich tract