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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGCAGATGCGGGTAACATTGAGGCTACTGTTGGCGGGGAATTCTTGCTGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcatggtgctcttggtaatccatgcatcttgatacgaactttctctgaatctggattgtacccactgctggatggtcactactcgtggaagtga...

Basic information

species Physcomitrella patens
transcript PP1S64_199V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S64_199V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA07G03230.1 (Glycine max), 5'ss of exon 2
---GAAAGCAGATGCGGGTAACATTGAGGCTACTGTTGGCGGGGAATTCTTGCTGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcatggtgctcttggtaatccatgcatcttgatacgaactttctctgaatctggattgtacccactgctggatggtcactactcgtggaagtga--
   | |   |||| | ||  | | |||  |  |      | | |  || ||||| |||||||||||||| |||||||| || ||  |||| |||||| |||||||| |  |    |||   |  |  || ||| ||||   |      | |   || || |   |  |    |       ||      |  |  ||    ||   
AATGCATAAAGATTCAGGAGAAAGTGAATCC-CAAAAAACAGAG--TTTTTGCTTAGAGTGGATGGTGGGGCAACTGTAAACAACCTGCTGATGCAGATTCAGgtttggactaattgcatattattttctatggatctctttgtttcatctaattgcatataattctt--ttaaaaaaaaataaaatttgttaatgatcatgtta

upper sequence: PP1S64_199V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv09s0002g07860.t01 (Vitis vinifera), 5'ss of exon 3
GAAAGCAGATGCGGGTAACATTGAGGCTACTGTTGGCGGGGAATTCTTGCTGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagt---tcatggtgctcttgg---taatccatgcatcttgatacgaactttctctgaatctggattgtacccactgc-tggatggtcactactcgtggaagtga
| | ||||  | |         |     | ||     |||||||||||||| ||||| ||||||||||||||  |||| ||| |  | |||||  |||||||| ||   |  || |  ||||||    |||   ||| || |      ||| |          ||| || ||    |||| | | |   |    || ||        
GGATGCAGGGGAGAAGGGTGAGGTCAAGAATGAGAAGGGGGAATTCTTGCTTAGAGTTGATGGTGGTGCAACCATTAACAATCTTTTGATGCAAATTCAGgttcgtattttctgctattcttggatccaatatctgcttcgttgctgtaacatgtaacagtaatggtttctattttctgcattgctaaacttctcttgtt-------
















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|162197251|gb|FC374202.1|FC374202
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
EST: gi|37827554|gb|BJ585566.1|BJ585566
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCCAGTGGTTAGACCAGTTGACATTGAGACTAC
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGT-CCAGTGGTTAGACCAGTTGACATTGAGACTAC
EST: gi|162197250|gb|FC374201.1|FC374201
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
EST: gi|162196069|gb|FC372721.1|FC372721
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
EST: gi|162170942|gb|FC346633.1|FC346633
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
EST: gi|100425541|gb|BY958647.1|BY958647
EST:     TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAG                         GCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA
genomic: TGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcat ... ttgcctgcagGCTGATTTACTTGGAAGTCCAGTGGTTAGACCAGTTGACATTGAGACTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGCAGATGCGGGTAACATTGAGGCTACTGTTGGCGGGGAATTCTTGCTGAGAGTGGATGGTGGTGCAACTGTTAATAATTTGCTTATGCAGCTTCAGgttagttcatggtgctcttggtaatccatgcatcttgatacgaactttctctgaatctggattgtacccactgctggatggtcactactcgtggaagtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT