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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT

Basic information

species Physcomitrella patens
transcript PP1S219_94V6.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g49110.2 (Oryza sativa), 3'ss of exon 7
gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgact-tgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT
                                                         |||   |  ||   |  |      | ||   |      |    | | | | || |   |  | | ||  |  | | | ||       |||| || || |  |   |||| |  ||||| || ||||| |||||||||||||||||||||||||| |||||||| || || ||    ||| | |||   |  |||   || ||||| |
--------------------------------------------------------gtctgtctcttctctagttctctttatattctgttttttatc--ttgatcaagtacct-tcacaagtgcaa--tagttgagtaacatagaaactgtctgtctcaatagGCACGTGCTGGTGCTGATGTAGTTAGCCCTAGTGACATGATGGATGGCCGTGTTGGAGCAATACGTGCTGCTTTGGATGCTGAGGGTTTCCATGATGTCT

upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT
                                                   ||| ||  |    | |  |               |      | ||    || ||      ||  | |  ||    ||    |||   | || |    || | ||      |||| |||||||||||||||||||| || |||||||| ||||||||||| || || || ||  | ||   |||||| |||   |  ||   |||  ||||||
---------------------------------------------------tgaggaaatatgcttttat-----------gttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttg-tctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT

upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA06G12110.1 (Glycine max), 3'ss of exon 7
gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT
                                                             |||  || | | |     |     | |  | | ||    || ||      ||| | |  ||    ||    |||   | || |    || | ||      |||| |||||||||||||||||||| || |||||||| ||||||||||| || || || ||  | ||   ||||||||||   |  ||   |||  ||||||
------------------------------------------------------------aaatcatcat-atgcttttatgttcccaatatctaaagtttccttgctacactc-tctataacaccactaacattttttttg-tctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTTGATGCTGAAGGCTTTCAGCATGTTT

upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 7
gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactg-cagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT
                                                     |   |    ||| | ||    |  | |  |||  |  |  |||   |  | || ||          || |  |   ||  |      || || |  |   || |    |||||| | || ||||||||||||||||| || ||||||||||||||||| ||||| || || || |||  ||||||||||   |  ||   |||| |||| |
-----------------------------------------------------actcttgacatttttgttgcttgaaaatgcat--attattcaat--gctgctatggc-------ctgactagtttgtgattctaccatgttggacctacttttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGTGTAGGAGCAATTCGAGCAGCTCTTGATGCTGAAGGCTTTCAACATGTGT

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|208397534|gb|DC916404.1|DC916404
EST:     TCATGNATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162270288|gb|FC447300.1|FC447300
EST:     ACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: ACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162179399|gb|FC355399.1|FC355399
EST:     ATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: ATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162270289|gb|FC447301.1|FC447301
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162166751|gb|FC342720.1|FC342720
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162152577|gb|FC328855.1|FC328855
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162250292|gb|FC425946.1|FC425946
EST:     CATGAATGACGAGACAGTACATCAGCTTTTGCA-GCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGC
genomic: CATGAATGACGAGACAGTACATCAGCTTT-GCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGC
EST: gi|162166620|gb|FC343512.1|FC343512
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGC
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGC
EST: gi|162150766|gb|FC327038.1|FC327038
EST:     CAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTG-TAGCCCTAGTGACATGATGGATGGGCGT
genomic: CAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162154906|gb|FC331948.1|FC331948
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGC
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGC
EST: gi|162179122|gb|FC355587.1|FC355587
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|208373778|gb|DC956294.1|DC956294
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|208396900|gb|DC915948.1|DC915948
EST:     TCATGNATGACGAGACAGTACATCAGC-TTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162150767|gb|FC327039.1|FC327039
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|208349261|gb|DC918011.1|DC918011
EST:     TCA-GAA-GACGAGACAGTACATCAGC-TTGCAAGCAGGCCGTAGNTCAG                         GCTCAAGCTGGAACAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162270867|gb|FC446896.1|FC446896
EST:     AGCAGGCCGTAGCTCAG                         GCTCAAGTTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: AGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
EST: gi|162156546|gb|FC332154.1|FC332154
EST:     TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAG                         GCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT
genomic: TCATGAATGACGAGACAGTACATCAGCTTTGCAAGCAGGCCGTAGCTCAGgtacgggttt ... ttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT
                                  atgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG