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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgtcacttttcaagagtgaacatatcacctagctctggatctaattgccagttttcatgcagcctggtagagcgattgtgcattcctagcggctcttcttgaggattttttctcactactcacaggacaagttcgattctcttgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA

Basic information

species Physcomitrella patens
transcript PP1S271_80V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S271_80V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaaatgtcacttttcaagagtgaacatatcacctagctctggatctaattgccagttttcatgcagcctggtagagcgattgtgcattcctagcggctcttcttgaggattttttctcactactcacaggacaagttcgattctcttgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA
|||   |    |||  |     |  |    |        |||  ||||||||   ||   |  | |    || ||||       | |||  |||  | |           | | |||               |   ||| |      |||||||| ||||||||||  || || ||| ||||  || |||| ||||| |||||||||||||||||||  ||||| |||   |       |||    |||||||  |||
gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaa------tacatggctaatgacgtcct------actctttt--------------atgtgttggcccaaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA
















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|208380288|gb|DC919124.1|DC919124
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|162245043|gb|FC421569.1|FC421569
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|162183314|gb|FC359229.1|FC359229
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|208357665|gb|DC934117.1|DC934117
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGA
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGA
EST: gi|162245042|gb|FC421568.1|FC421568
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|162266011|gb|FC442696.1|FC442696
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|208352193|gb|DC901714.1|DC901714
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|208367659|gb|DC947365.1|DC947365
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|162183315|gb|FC359230.1|FC359230
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|37834787|gb|BJ592799.1|BJ592799
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|100439177|gb|BY980132.1|BY980132
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGC
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGC
EST: gi|162266010|gb|FC442695.1|FC442695
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
EST: gi|162204856|gb|FC381187.1|FC381187
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATAC
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATAC
EST: gi|18339530|gb|BJ171557.1|BJ171557
EST:     GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTG                         GTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG
genomic: GACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATG

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

GTACAATTTGCTGCTGGGAGGGACTTGAGACCAGGTCAGCTCGACAATATGATCGCAACATTGGCAAACTGgtaaaatgtc ... tgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaggattttttctcactactcacaggacaagttcgattctcttgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA
                                       ttctctt  CT-rich tract
       attttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgtcacttttcaagagtgaacatatcacctagctctggatctaattgccagttttcatgcagcctggtagagcgattgtgcattcctagcggctcttcttgaggattttttctcactactcacaggacaagttcgattctcttgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA