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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaacaatgtcaaagttgtagcttatgcttgattttctagttttttgagatttgaacactcatcattgtgcttaatgcccggttttgctgtttagtcctgggagggctccacttgacttgagacttcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAGGATGCGCTGAACGCTACCAAAGCCGCCGTGGAGGAAGGTATCGTTGTGG

Basic information

species Physcomitrella patens
transcript PP1S15_485V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EDP03982 (Chlamydomonas reinhardtii), 3'ss of exon 12
gtactaacaatgtcaaagttgtagcttatgcttgattttctagttttttgagatttgaacactcatcattgtgcttaatgcccggttttgctgtttagtcctgggagg-gctccacttgacttgagacttcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAGGATGCGCTGAACGCTACCAAAGCCGCCGTGGAGGAAGGTATCGTTGTGG
                                    | || ||    | | ||         || |||| | ||   |     |   |         | || |  |   ||    | | |||  | ||      |||||||||| || || || ||||| ||  | |||||||||||||| || || ||||| || |||||||| ||||| ||||| |||||||| || || ||  | |
---------------------------------cgctgtcaagcagctagcgagggcggtg-tcttcatcg-gcagcagatttgaagtaaggaccctgaccagcaatatgccattcctcactctaaacac----tgcagGTGGGCGCCCAGACCGAGACGGAGCTCAAGGAGAAGAAGCTGCGCGTGGAGGACGCCCTGAACGCCACCAAGGCCGCTGTGGAGGAGGGCATTGTCATCG
















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|162166112|gb|FC343381.1|FC343381
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|67508408|gb|BJ941275.1|BJ941275
EST:     ATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: ATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162184149|gb|FC358895.1|FC358895
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162219401|gb|FC396918.1|FC396918
EST:     GTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: GTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162182314|gb|FC357185.1|FC357185
EST:     CCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: CCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162179103|gb|FC356504.1|FC356504
EST:     GGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAA-TGAAGGGAG-AGAAAGCTCCGTGTTG
genomic: GGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAA-GGAGAAG-AAGCTCCGTGTTG
EST: gi|162174052|gb|FC350567.1|FC350567
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162186556|gb|FC363320.1|FC363320
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162226061|gb|FC401027.1|FC401027
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162198440|gb|FC375275.1|FC375275
EST:     GGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAA-TGAAGGGAGAAGAAGCTCCGTGTTGA
genomic: GGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAA-GGAGAAGAAGCTCCGTGTTGA
EST: gi|162161063|gb|FC337048.1|FC337048
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162191124|gb|FC367386.1|FC367386
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162153514|gb|FC329608.1|FC329608
EST:     GCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGATTTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: GCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162150358|gb|FC326630.1|FC326630
EST:     GGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: GGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162179104|gb|FC356505.1|FC356505
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162198441|gb|FC375276.1|FC375276
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
EST: gi|162177440|gb|FC352973.1|FC352973
EST:     AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAG                         GTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG
genomic: AGTTGAATGAGAGAATTGCTAAGTTGTCTGGAGGTGTGGCCATCATTCAGgtactaacaa ... tcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgctgtttagtcctgggagggctccacttgacttgagacttcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAGGATGCGCTGAACGCTACCAAAGCCGCCGTGGAGGAAGGTATCGTTGTGG
                              acttgac  putative branch site (score: 4)
                                           cttcctgt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaacaatgtcaaagttgtagcttatgcttgattttctagttttttgagatttgaacactcatcattgtgcttaatgcccggttttgctgtttagtcctgggagggctccacttgacttgagacttcctgtgcagGTGGGAGCTCAAACTGAGACAGAATTGAAGGAGAAGAAGCTCCGTGTTGAGGATGCGCTGAACGCTACCAAAGCCGCCGTGGAGGAAGGTATCGTTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA