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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC

Basic information

species Physcomitrella patens
transcript PP1S243_67V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                                                                   |||   |    ||  ||||   |   | |  |    |   | |  | |   ||    || ||||| |  || |      |   |||||||  |   |  | ||||||||||| |||||||||||||| ||||| || || || ||||| |||||| |||| ||||| |||||||| ||| |||| || || ||  |  | ||  
-------------------------------------------------------------------agggatttacacagatattgtcgagaatattttatgaaattcctatgc---ttgaaggttgaagtatttct-caccatgtgtttttttaaaatgtcgaatgcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttc-agttcatttttctcgtcgaagtttggctgcttttctta-catttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                                                                         |   | |    |  || |    |   |  |||| | | || | ||  |||         |||      | || |||  | | |   | ||   ||| ||||||||||| |||||||||||||||||||| || || || ||||| || || |||||||| |||||||| || ||||||||||| |||||  | |||||  
-------------------------------------------------------------------------tctctaaaagctaactttgggaattcctatagtttcctagattataattcctactagttttttttatttcttattagtaatgtggttatttatgttgcagATGGATGGGTTTGATCAAACAGTCAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTTTGTTGCGTCCTGGTAGACTTGACA

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                                                                 |||   |  |  |  |  | |||   ||||   ||  |||  |  ||||| |  |     |     ||| | | ||| | |   | | ||  | |    ||||||||||||||| |||||||||||||| ||||| || || || ||||| || || |||||||| |||||||| || ||| ||||||| |||||  | |||||  
--------------------------------------------------------------tctctaaaagcaaacttttggagttcca-acagttttc--tagattatagttcctactagctct-----ttttgtttcttat-tagtaatgttgttatctatgttacagATGGATGGGTTTGATCAAACAGTGAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTCTGTTGCGTCCTGGTAGACTTGACA

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
----gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtgg---acctcctaggtg-----atagatca---tttatttctgtacagaactcggtagtct-tcagttcatttttctcgtcgaagtttggctgcttttcttacatt--tttaatgttctggt------tacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
     |||||| |  | || || | |  ||  | ||  |     ||   | |    | | ||     |  ||  | | |      |  || |   ||| ||||| |  |   || | || |   |  |   |   ||| |   ||  || |     || |      ||  ||||||   ||| |      | ||||||||||||||||| |||||||| ||||||||||| || ||||| || ||| | ||||| ||| | ||||| ||| ||||||| |||||| | |||||||
gtatctatgaaatgatatttatgt-taggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
--------------------gtatgaagtctttttaatttctcagtttt-ttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacag--aactcggtagtcttcagttcatttttctcgtcgaagtttg--gctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                     ||| | ||  | | | | | |   |  |  | |  | ||   | | |        | ||       |  ||  | | | || | || |  |  ||  |  | | | | || || |||  | |  |  | ||  ||    |  |  ||  ||  |||     |  | |  || ||||||||||||||||| |||||||| ||||||||||| || ||||| || ||| | ||||| ||| | ||||| ||| ||||||| |||||| | |||||||
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttctt-cagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
       || | | | |      | |  | | ||||     | |  |  | |  |  ||  |  |     | |    | | | || |||   |      | ||         |||| || |||| |  |  | ||| |  ||   |||  |   |  | || |   ||||||||||||||||||| ||||| || ||||||||||| || ||||| || ||| | ||||| ||  | ||||| ||| ||||||| |||||| | |||||| 
------ggtgtctatga------aatgatatttctgttagcttctgtgattatgttttgtgctact---attagtacttactaatatctcc-cgagctgcagtgaatcagttttcacttatctc-ttaatctctggttatttggtttaattacctgttctttt--ctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAACAGAGCAGACACCTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGAT-

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggt----tacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                                                                                                                            ||  |||     | |  |    ||      | | || || ||      |||||||||||||| |||||||| || ||||| || || ||||||||||| ||||| || || ||| | || |||||  | ||||| || ||| | |||||  
----------------------------------------------------------------------------------------------------------------------------gtaaaagg--aaccgagtagagtaagccgctgacgtccttgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggt----tacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                                                                                                                            ||  |||     |    |    ||      | | || || ||      |||||||||||||| |||||||| || ||||| || || ||||||||||| ||||| || || ||| | || |||||  | ||||| || ||| | |||||  
----------------------------------------------------------------------------------------------------------------------------gtaaaagg--aaccaagtagagtaagccgctgacgtccttgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

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|208371413|gb|DC955749.1|DC955749
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|37836792|gb|BJ594800.1|BJ594800
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|37832462|gb|BJ590474.1|BJ590474
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|37845653|gb|BJ603661.1|BJ603661
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|208376580|gb|DC952307.1|DC952307
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|208367978|gb|DC951003.1|DC951003
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|162164770|gb|FC340492.1|FC340492
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|67724576|gb|BJ974835.1|BJ974835
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|208398297|gb|DC916436.1|DC916436
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|37851697|gb|BJ609705.1|BJ609705
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|208387168|gb|DC945467.1|DC945467
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|37832812|gb|BJ590824.1|BJ590824
EST:     CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
EST: gi|162186124|gb|FC361328.1|FC361328
EST:     CGTATCCTTATGGAACTTCTGAATCAG                         ATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC
genomic: CGTATCCTTATGGAACTTCTGAATCAGgtatgaagtc ... ctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC
                        ttttcttacattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacagATGGATGGTTTTGATCAAACAGTCAATGTTAAAGTGATCATGGCTACCAACCGGGCAGATACTCTAGACCCCGCTTTGTTGCGACCTGGACGTCTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT