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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgagacagtgagatggcctctttatcgcggacgctattgtatggtcgttctgtgtcttcagtggtgtttactgaattattatgtaattgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG

Basic information

species Physcomitrella patens
transcript PP1S138_33V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S138_33V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G045371_T02 (Zea mays), 3'ss of exon 4
agttgagacagtgagatggcctctttatcgcggacgctattgtatggtcgttctgtgtcttcagtggtgtttact-gaattattatgtaa---ttgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG
  |    | |||  |||    |  || |  | |   ||| ||| |    | |    ||| | |    | |||| |  ||| || ||  |    ||  | || ||| |  |||| ||||||||||| || |||||||| || ||||| ||||| |||||||| || ||||| |||||||| || ||  ||
--tatttatagttggata--ttgcttgttccagttcctagtgttttagtgcttgtagtcatgacctttatttatttaaatgatcatccatgctttactatgcagGGAGCTGGCCAAGGATTTTGTTGTTTCTGGAACAGCATCAGAATCTTTGTATGGTGCTTGTGAATCCATGTACAAGCCGGACATG

upper sequence: PP1S138_33V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 3
---agttgagacagt-gagatggcctctttatcgcggacgctattgtatggt-cgttctgtgtcttcagtggtgtttactgaattattatgtaattgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG
    ||| || | || || ||    || |||   |  |  ||    |    |  |  || | |     ||  |  |||    | ||||   |  || |||   ||| || | ||||| |||||||||||||| || ||||||||||||||  | |||||||| || || || ||||| || ||  |  ||
taatgttaagcctgttgaaattcgttccttacatcctatactgacttgccatatggcctctctaccttgtaat-cttatcagagtatttcctt-ttattc---agGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG

upper sequence: PP1S138_33V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 4
agttgagacagtg-agatggcctctttatcgcggacgctattgtatggtcgttctgtgtcttcagtggtgtttactgaattattatgtaattgttctgaagGCA----ATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG
   ||||    |  | ||    |  |||     |  |  ||| ||  |        |   | || |||||   | ||  ||      |  |   ||| || |||     || || || |||||||| ||||| |||||||||||||| ||| ||||||||||||| ||| | |||| |||||| ||| ||
---tgagctgatttaaatatgattcttaatatagttgagattttaccga-acatgatagttgcaatggtgagca-tgccttgacgcttgttctctctaaatgcagGGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATG

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|37836001|gb|BJ594011.1|BJ594011
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|37853577|gb|BJ611585.1|BJ611585
EST:     ACGATGACGGAACTCCTTTTATTCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: ACGATGACGGAACTCCTTTTA-TCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|100419788|gb|BY957712.1|BY957712
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208367915|gb|DC950968.1|DC950968
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|18342551|gb|BJ174586.1|BJ174586
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTAT
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGG-ATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTAT
EST: gi|162252674|gb|FC428711.1|FC428711
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|18360212|gb|BJ192274.1|BJ192274
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAA
EST: gi|18343929|gb|BJ175967.1|BJ175967
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|6227534|gb|AW156133.1|AW156133
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208362480|gb|DC930985.1|DC930985
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|100440924|gb|BY962412.1|BY962412
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCCGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|18349035|gb|BJ181084.1|BJ181084
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208387202|gb|DC945501.1|DC945501
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|37821692|gb|BJ579758.1|BJ579758
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|37823121|gb|BJ581187.1|BJ581187
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208363882|gb|DC943339.1|DC943339
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208385390|gb|DC953051.1|DC953051
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
EST: gi|208391649|gb|DC937909.1|DC937909
EST:     AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAA                         GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA
genomic: AACGATGACGGAACTCCTTTTATCTGCACCACTGATTTAATCGGTGCCAAgtaacgcact ... tgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcgttctgtgtcttcagtggtgtttactgaattattatgtaattgttctgaagGCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTG
                                            ttgttct  CT-rich tract
                        tttactgaattattat  TA-rich tract