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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttttgttcagtaccaacttttacctctatataatttgcctattacaaagttttgatctgcggtctattgggtttccactcttaatgttcaata...

Basic information

species Physcomitrella patens
transcript PP1S31_338V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G062210_T02 (Zea mays), 5'ss of exon 3
--------------AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttttgttcagtaccaacttttacctctatataatttgcctattacaaagttttgatctgcggtctattgggtttccactcttaatgttcaata--------
              || ||||| |||||||| ||||||||||| || ||| ||||||| || ||||||||  | |||||| |  |||| |||||||| |||||| |   |   ||||      ||| |   ||  |   | | || ||| | |    |  |   ||  |  |||||   ||   ||  |  |   || |         
CGCATTTTGCATAGAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAGgtataatgcta--tcagattagccttgtgtatcattgacaatcgc-tatcata----tcagtgttgttgattattgcacttat-cttgtggtaaacagtgcagccgtg

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G062210_T01 (Zea mays), 5'ss of exon 4
AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttttgttcagtaccaacttttacctctatataatttgcctattacaaagttttgatctgcggtctattgggtttccactcttaatgttcaata--------
|| ||||| |||||||| ||||||||||| || ||| ||||||| || ||||||||  | |||||| |  |||| |||||||| |||||| |   |   ||||      ||| |   ||  |   | | || ||| | |    |  |   ||  |  |||||   ||   ||  |  |   || |         
AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAGgtataatgcta--tcagattagccttgtgtatcattgacaatcgc-tatcata----tcagtgttgttgattattgcacttat-cttgtggtaaacagtgcagccgtg

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT3G61140.1 (Arabidopsis thaliana), 5'ss of exon 4
AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttttgttcagtaccaacttttacctctatataatttgcctattacaaagttttgatctgcggtctattgggtttccactcttaatgttcaata--------
   ||||| |||||||| ||||||||||| ||||| |||||||| || ||||| ||| | || || ||| | || || ||| | |||| ||  | || ||    |||||   |  | ||||| |   |||| ||  || || ||   | |   |  |||  || ||   | | | |||   || ||        
CAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAGgt-tgcatattctt----accaagactctcgtctattt--cttgcatagcaccaaattactaaccttgaactaa-ggattattagtgtgaatacccactaagaccaga

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|37845778|gb|BJ603786.1|BJ603786
EST:     NNGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|67726052|gb|BJ976311.1|BJ976311
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|37851742|gb|BJ609750.1|BJ609750
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|162223424|gb|FC400315.1|FC400315
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|162200332|gb|FC376643.1|FC376643
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|162223425|gb|FC400316.1|FC400316
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|37836464|gb|BJ594472.1|BJ594472
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|208382267|gb|DC919255.1|DC919255
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTNGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|37847958|gb|BJ605966.1|BJ605966
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|37842497|gb|BJ600505.1|BJ600505
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|162200333|gb|FC376644.1|FC376644
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|37846187|gb|BJ604195.1|BJ604195
EST:     NNGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
EST: gi|67728119|gb|BJ978378.1|BJ978378
EST:     TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG                         TCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT
genomic: TTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATT

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: 35 (upstream exon), 31 (downstream exon)
Score: 6

AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttt ... ttttttgcagTCGATATGCTTCTTGCTTAGGGTATTTGCAAAAGCTGAAACCGAATTTATTGCTCGATATTCATCTATACGATCATGTGGAGACATTATATGAGCAAATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAGgtatgagttttgttcagtaccaacttttacctctatataatttgcctattacaaagttttgatctgcggtctattgggtttccactcttaatgttcaata

- - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT