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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagttttctaccatggtcatctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA

Basic information

species Physcomitrella patens
transcript PP1S234_26V6.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 2
tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagtt--ttctaccatggtcatctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA
                   |   ||  ||||  || |||     |   ||   | | |||  | ||   |  | || |  | |   |  | |     |  ||||||| ||||||| ||||| ||||| ||||| ||||||||||||    | || |||||||| || ||| | || ||||||||
------------------gtaagaatcttgtgcttcttctgctcacatgtaaatgccacccggctcgcttatacttggcttct---ttttaaaattttgtagATATTAGGGAGCTCATATCATTGGATGATGTCATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGA

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 2
tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagttttctaccatggtcatctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA
                    | |  || |  |  |  | |    || | |  ||  |     ||   |  | || |  | ||     |  ||   |  ||||||| ||||||| ||||| ||||| ||||| ||||||||||||    | || |||||||| || ||| | || ||||||||
-------------------gtaaggatcttctcgtgcttgtgtaaatattgatcggc-----tcgcttatacttggcttctgttaaattttt---tgtagATATTAGGGAGCTCATATCATTGGATGATGTCATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGA

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G12790.4 (Arabidopsis thaliana), 3'ss of exon 3
tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagttttctaccatggtc-atctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA
               ||  |  | ||   |||  || | | || |  |  |||       | |     ||  | ||   |||      || ||| || |||||||  | || || || |||||||||||||| |||||||| || || ||||| || |||||||  ||| |||| ||||||||
--------------gtgagtgaagaa---gtttcttcttgttcaattacctttggggggagttttgagtgcttctcacttttttgacatcgttgaatgcagATATCAGAGAACTTATTTCTTTGGAAGATGTGATGGAGGATCTAAAGCTTGGTCCTAATGGTGCCCTTATGTATTGCATGGA

upper sequence: PP1S234_26V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 3'ss of exon 2
--tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagttttctaccatggtcatctgaatttcgagt--ttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA
    | | |||    |            ||| || |||||  ||    |            || |  | |   ||  |||   |    |  |  || | | |||||||| |||||||  | || ||||| ||||| |||||||| |||  ||| |||||||||||||| ||| |||||||||||||
gtaagtagaattctttgcctgggaggtttttttttttttttcatttggggtggggtgggtttgtttctttagtttcagagcaatgaagtattgttttcttgcagATATTAGGGAGCTTGTTTCCTTGGATGATGTTATGGAGGAGCTTGGACTGGGGCCAAATGGTGGCCTTATGTACTGCATGGA

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|100430653|gb|BY978328.1|BY978328
EST:     AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCG                         ATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
genomic: AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCGgtgagtattc ... ttgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
EST: gi|67572391|gb|BJ945215.1|BJ945215
EST:     AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCG                         ATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
genomic: AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCGgtgagtattc ... ttgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
EST: gi|18368645|gb|BJ200730.1|BJ200730
EST:     AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCG                         ATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
genomic: AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCGgtgagtattc ... ttgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
EST: gi|100399107|gb|BY954203.1|BY954203
EST:     AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCG                         ATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
genomic: AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCGgtgagtattc ... ttgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
EST: gi|18350386|gb|BJ182437.1|BJ182437
EST:     AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCG                         ATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG
genomic: AGTGAACTTGGACCCAGCTGCTGACCACTTCGAGTATCCTGTCTCCGTCGgtgagtattc ... ttgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttttctaccatggtcatctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA
                      tgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgcataatcgagtatggattgaaaatttgttatttttcgatcgaagagttttctaccatggtcatctgaatttcgagtttggatgctcattgcatacagATATTCGGGAGCTAATATCTTTGGAAGATGTAATGGAGGAACTTAAACTTGGGCCAAATGGTGGTCTTGTGTACTGCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA