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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctctatctgcccaggccttagattgagttacatttctttgttttcaattctgcccggaccgttgttatcattgattaatgtgtccttgtgttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATGGACGGCCGCTTTGTGCCCAACATCACAATCGGTCCTCTTGTTGTGGATG

Basic information

species Physcomitrella patens
transcript PP1S39_426V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_426V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G178960_T01 (Zea mays), 3'ss of exon 2
gctctatctgcccaggccttagattgagttacatt-tctttgttttcaattctgcccggacc-gttgttatcattg-attaatgtgtc-cttgtgttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATGGACGGCCGCTTTGTGCCCAACATCACAATCGGTCCTCTTGTTGTGGATG
     |       ||||  |||| | ||     || |   | || |  || |   | ||    | | || || ||  |||    |     ||   | ||  ||| | ||||| || ||    || |||||||| |||||||| ||||| || |||||||| ||||||||||| || |||||||| || ||| | ||||| ||||
----caataaataaggcaatagagtaagcactgttatgcattttcttgatgccaactggcttagattttgtctttatattgccattctgtttacatattactagGTAAAAGCCGTGGAGGTGGCAGGATGTGACTGGATTCATGTCGATGTCATGGACGGGCGCTTTGTGCCAAATATCACAATTGGACCTTTGGTTGTTGATG

upper sequence: PP1S39_426V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT5G61410.2 (Arabidopsis thaliana), 3'ss of exon 2
gctctatctgcccaggccttagattgagttacatttctttgttttcaattctgcccggaccgttgttatcattgattaatgtgtccttgtgttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATGGACGGCCGCTTTGTGCCCAACATCACAATCGGTCCTCTTGTTGTGGATG
                       | |  ||   || || |  | |    | | |  |     ||||| ||     || |  | |    |  || |   || | ||||| || ||    || || |||||||||||||| || || || |||||||| || ||||| |||||||| || ||||| ||||| || || ||||
----------------------gtaggtttttgttgctctcctctttggttt-cttgtgtgtttgtt-tctccatttcac-tatttccggcttctttcagGTAAAAGCAGTGGAGTTGGCAGGTTGTGATTGGATTCATGTTGATGTCATGGACGGTCGTTTTGTTCCCAACATTACTATCGGACCTCTCGTGGTTGATG

upper sequence: PP1S39_426V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP05517 (Chlamydomonas reinhardtii), 3'ss of exon 1
----------------------gctctatctgcccaggccttagattgagttacatttctttgttttcaattctgcccggaccgttgttatcattgattaatgtgtccttgtgttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATGGACGGCCGCTTTGTGCCCAACATCACAATCGGTCCTCTTGTTGTGGATG
                       |  |   |||    ||  |     |     |    ||   | |  ||    || ||| || |      |  | |||  | |  ||| |     | | || |    ||  | ||  | ||||| || || ||| | ||| ||||||| |||||||||||||| |||||||||||||| ||||| || || || || || |
gtgcgtcgcgcgggcccaacaaaccttgcttgcatgtgcgctccgccg--ccgcggcgctcgctgtagaagagcgcgcgggccctgaacccctctaatttgt-tcccctcga----taacagGTGCGCGCCATCGACCAGGCCGGCTGCGACTGGGTGCACATCGACGTTATGGACGGCCGCTTCGTGCCCAACATCACCATCGGCCCGCTGGTCGTCGAGG

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|208380177|gb|DC927456.1|DC927456
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|208354171|gb|DC957405.1|DC957405
EST:     TCGTTTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162280157|gb|FC455966.1|FC455966
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|208378510|gb|DC927207.1|DC927207
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|208392822|gb|DC957089.1|DC957089
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162264352|gb|FC440518.1|FC440518
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162242348|gb|FC418899.1|FC418899
EST:     CTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: CTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|208381445|gb|DC927881.1|DC927881
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162228610|gb|FC405430.1|FC405430
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162224842|gb|FC401050.1|FC401050
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162250799|gb|FC426843.1|FC426843
EST:     CTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: CTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
EST: gi|162253040|gb|FC429101.1|FC429101
EST:     TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAG                         ATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG
genomic: TCGTCTCGCCCTCGATTCTATCAGCCAACTTCGCCATCCTGGGAGACCAGgtactttggt ... gttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattctgcccggaccgttgttatcattgattaatgtgtccttgtgttttgatagATCAAAGCTGTTGAAAACGCCGGATGTGATTGGATTCACGTCGACGTGATGGACGGCCGCTTTGTGCCCAACATCACAATCGGTCCTCTTGTTGTGGATG
                            gattaat  putative branch site (score: 3)
                    ttatcattgattaat  TA-rich tract