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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacgaacggacagcataatactatacagccaaaatgcggattctactgaaccatttcggattcggggtcattctttaacgcattgctctgcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCTGGATTTGACCAAGGCCATCATGGATAAGGCTCCGGGGAAGCTCCGCTTA

Basic information

species Physcomitrella patens
transcript PP1S91_92V6.2
intron # 2
splice site 3'
intron type U2

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|162266704|gb|FC442857.1|FC442857
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162191712|gb|FC367445.1|FC367445
EST:     GAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|67720384|gb|BJ970643.1|BJ970643
EST:     CTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTT-GGAATTTCAGTGCCAGATGAATCTGCGCT
genomic: CTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162235775|gb|FC411078.1|FC411078
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208351218|gb|DC918105.1|DC918105
EST:     AAGATTA-TGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: AAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162192896|gb|FC371437.1|FC371437
EST:     GAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208394444|gb|DC928496.1|DC928496
EST:     TTCAAGANTATTGACATCNATGGCTCCGAGTGCTT-CTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGNAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|67697844|gb|BJ958077.1|BJ958077
EST:     CCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTTCAGTGCCAGATGAATCTGCGC
genomic: CCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAA-TTTCAGTGCCAGATGAATCTGCGC
EST: gi|208381246|gb|DC919136.1|DC919136
EST:     TGACATCAAT-GCTCCGAGTGC-TNCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162275940|gb|FC452008.1|FC452008
EST:     GAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162265823|gb|FC442410.1|FC442410
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208380200|gb|DC927479.1|DC927479
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208381756|gb|DC928419.1|DC928419
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208367395|gb|DC951299.1|DC951299
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162225297|gb|FC402063.1|FC402063
EST:     ACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: ACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208376539|gb|DC922570.1|DC922570
EST:     TCAAGANTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACA-G                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|15261780|gb|BI437090.1|BI437090
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162247154|gb|FC423030.1|FC423030
EST:     CCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: CCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208368220|gb|DC951500.1|DC951500
EST:     TCAAGATTATTGACATCAATGGCTTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TCAAGATTATTGACATCAATGGC-TCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208385198|gb|DC923578.1|DC923578
EST:     TTCCTTACCCGCACAGG                         TTACACAGGTGNAGATGGTTTCGAAATTTCAGTGCCAGATGAATTTGCGCT
genomic: TTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208380284|gb|DC919120.1|DC919120
EST:     TTCAAGATT-TTGACATCAATGGNT-CGAGTGNTT-CTTACCCGCACA-G                         NTACACAGGTGAAGATGGTTTNG-AATTTCAGTGCCAGATGAATTTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162239713|gb|FC417112.1|FC417112
EST:     GAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162275941|gb|FC452009.1|FC452009
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208396769|gb|DC929064.1|DC929064
EST:     AGATTA-TGACATCAA-NGCTCCGAGTG-NTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATTTGCGCT
genomic: AGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162154827|gb|FC331141.1|FC331141
EST:     CAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: CAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208370913|gb|DC944288.1|DC944288
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGNTT-CTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATNTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162266703|gb|FC442856.1|FC442856
EST:     GAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162205059|gb|FC381768.1|FC381768
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162252065|gb|FC428304.1|FC428304
EST:     AGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: AGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162175930|gb|FC351608.1|FC351608
EST:     GTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: GTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208351885|gb|DC917946.1|DC917946
EST:     TTCAAGATT-TTGACATCAAT-GCTCCGAGTGCTT-TTTACCCGCACAGG                         TTACACAGGTGAAGATGG-TTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162240599|gb|FC414410.1|FC414410
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162170224|gb|FC347344.1|FC347344
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162149930|gb|FC326253.1|FC326253
EST:     AGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: AGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162215801|gb|FC390866.1|FC390866
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162180786|gb|FC358287.1|FC358287
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208398845|gb|DC920793.1|DC920793
EST:     TTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATNTGCGCT
genomic: TTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|19788881|gb|BQ040978.1|BQ040978
EST:     TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGG                         TTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGATTATTGACATCAATGGCTCCGAGTGCTTCCTTACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|208353157|gb|DC921859.1|DC921859
EST:     ACCCGCACAGG                         -TACACA-GTGAAGATGGTTTNG-AATTTCAGTGCCAGATGAATTTGCGCT
genomic: ACCCGCACAGGgtatgtcctc ... gcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgaaccatttcggattcggggtcattctttaacgcattgctctgcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCTGGATTTGACCAAGGCCATCATGGATAAGGCTCCGGGGAAGCTCCGCTTA
                            ctttaac  putative branch site (score: 3)
                         attctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacgaacggacagcataatactatacagccaaaatgcggattctactgaaccatttcggattcggggtcattctttaacgcattgctctgcggatgcagTTACACAGGTGAAGATGGTTTCGAAATTTCAGTGCCAGATGAATCTGCGCTGGATTTGACCAAGGCCATCATGGATAAGGCTCCGGGGAAGCTCCGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA