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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatatttctagaatggcttggaagtttccactacctagagtgatcttgataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA

Basic information

species Physcomitrella patens
transcript PP1S100_124V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
--aagatatttctaga-atggcttggaagtttccactaccta-gagtgatcttg-ataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA
   ||| |  |   |   | || |     |  |   | |  |  | | || ||| | || || |  | |  |  | |    | || |       | |     ||| ||||||||  ||||  |  ||||| | || || || || |||||||||||||| ||||||||||| || |||||| ||||   |||    || ||||| 
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaa-----ggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------aagatatttctagaa----tggcttggaagt--ttccactacctagagtgatcttgataaattttcttgtagtaaaag----gacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA
                                                     |    | || |||    ||  |||  | |   ||||  |   | |     | || | |||||  ||  |   |        | | ||| |     ||  |   |||||||||||||  |  ||| |  ||    | |  || ||||||||||| || |||||||||||||| ||||| ||||||| ||  |  ||  | ||||| || 
gtgagtgatttattaattattaatctatcttacttattcttttaagtgcatttgtccgtgctggaagatctgatttgctactaactccaaaaagcatatcagacctgttgaatttaatttcaaacatgcttttaatagcca-acagtaaatgttcatgcagGTTTGAGGGAATGGAGGCACCTAATTCAAAATCTTTTTTCACAGAGATAATTGCTTCAATTTCAGACATTAAGTTTGGAAAGGACGGAAGATACATACTT
















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|15728932|gb|BI741051.1|BI741051
EST:     CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCT                         GTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
genomic: CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCTgtatgttcct ... ttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
EST: gi|7648411|gb|AW739394.1|AW739394
EST:     CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCT                         GTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
genomic: CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCTgtatgttcct ... ttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
EST: gi|15730306|gb|BI741781.1|BI741781
EST:     CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCT                         GTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
genomic: CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCTgtatgttcct ... ttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
EST: gi|162182432|gb|FC358031.1|FC358031
EST:     CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCT                         GTTTGAGGAGAATGAGCCGGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
genomic: CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCTgtatgttcct ... ttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
EST: gi|67725006|gb|BJ975265.1|BJ975265
EST:     CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCT                         GTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT
genomic: CGCCTCATCGATATGCGTCAATCAGCCTTATGTGATCGACACTCAAAGCTgtatgttcct ... ttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA
 tcttgat  putative branch site (score: 4)
     ataaattttcttgtag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatatttctagaatggcttggaagtttccactacctagagtgatcttgataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG