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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaatacattctcagtgcagcccaatcttcatgaatgacccctgcccactatagaggcgcaggttagtcatgtggtaggagtggtctcactttacttaggtttatttaggaagatgttctgagtttatacgtggctttctgaactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA

Basic information

species Physcomitrella patens
transcript PP1S323_70V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 3
gtataaaatacattctcagtgcagcccaatcttcatgaatgacccctgcccactatagaggcgcaggttagtcatgtggtaggagtggtctcactttacttaggtt-tatttaggaagatgttctgagtttatacgtggctttctgaactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA
                                                        | |  | ||  || |  |  |   |   ||  | | | |||    ||     ||   | |  ||  | ||| |    |  ||   | |     |  |||||| || || |||||||| || |||||| ||   || |||   ||| |  | |||   |||||||||||||||||| |||| |||||| ||||||| ||||
------------------------------------------------------gaaaacccacaa-ttggaaacttatcatctgtcctttgagtttttacagaccacatggtgtataataatatgactaatcaaatgcaatgcacgtatg-ccagCCTTTCAGGGACATGATAGAAGGGATGCGGTCAGACCTCAGAAAGACTAGATACAAGAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 3
gtataaaatacattctcagtgcagcccaatcttcatgaatgacccctgcccactatagaggcgcaggttagtcatgtggtaggagtggtctcactttacttaggtttatttaggaagatgttctgagtttatacgtggctttctgaactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA
                                     | |||||       |   ||   | ||   |||||  | || ||  |    | |     |||  ||      |||  ||  | ||   | |  |||  ||   || ||       |||||||| || |||||||| || ||||||||||  |||||   |||| |  ||||   ||||||||||||||||||| |||| |||||| ||||||| ||||
------------------------------------aagtgaccgagagaaaac-tatctgtgccacttagtggtttgata--aactatgttgtgataccaag------ttaccaacgt-tttgaaatcaataaatg---ttgtgg------cagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA
















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|162195318|gb|FC370839.1|FC370839
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162196412|gb|FC373558.1|FC373558
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162213600|gb|FC389680.1|FC389680
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAG
EST: gi|162263003|gb|FC438811.1|FC438811
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162167423|gb|FC343126.1|FC343126
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATC
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATC
EST: gi|162221129|gb|FC397770.1|FC397770
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162178499|gb|FC354951.1|FC354951
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162279509|gb|FC455820.1|FC455820
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
EST: gi|162162258|gb|FC338040.1|FC338040
EST:     TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAG                         CCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG
genomic: TTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGG

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), 35 (downstream exon)
Score: 26

ATGGGAGGATAGACTGGAAGATATCTTCTGCGGCCAACCTTATGACATGCTTGACGCTGCCCTCGCAGACACCGTCTCCAAATTTCCAGTCGACATTCAGgtataaaata ... aactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggtttatttaggaagatgttctgagtttatacgtggctttctgaactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA
     ttattta  TA-rich tract