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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattctgtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat...

Basic information

species Physcomitrella patens
transcript PP1S58_148V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G061620_T02 (Zea mays), 5'ss of exon 6
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaag--tgcacgcttatcattctgtaactgtaaacgaaatttg---tggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat
| | || |||||||| || |  |||||| | ||||||||| | |||||  | || ||||| | ||||||||| ||||| ||||| ||||||||||||||||||||  ||     || || |  |     | ||  |   |  ||   || |  || |  ||| |||  | ||  |     || |   |  || |||  || ||  
TCTTGAAATGGGTGGCGGGACATGGGATAGAGACACTGTACTACGTGCTCTGCGGGCTGCGTACAACAATCCAGAGCGTGCTGTTGAGTACTTATATTCTgtaagaatgattctttgtcctcgttactttctaggccttacatgcgatgaactttcagcgatttat--gtgtgcccaggtacgtttaac-tagtgaa-cacatc-

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 6
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattctgtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat--
| | || |||||||| ||||  ||||| ||||| ||||| || |||||  |||||||||||| ||| || |||||| ||||| | || ||| | ||||||||||||      ||| | || |     | | || | |  |||  | |      ||        | ||   ||     ||   || |  |||   | ||    
TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgttaactttattattttatcaatgca--ttgcagcttcattctgcctctgatgtgttcatttgtttcttttattttctgaaaaacatgctg

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G105772_T01 (Zea mays), 5'ss of exon 6
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgc-acgcttatcattctgtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacac-ctcagatgtattgagtca-tatat-
| | || |||||||| || |  |||||  | ||||||||| | |||||  | || | ||| |  ||||| || ||||| ||||| ||||||||||||||||||||    |  |||     ||  |  ||     | |    | |   |||  ||||| |  |||    | ||       | || ||  ||| |   | |  || 
TCTTGAAATGGGTGGCGGGATATGGGACAGAGACACTGTACTACGTGCCCTGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatgattctttgtcctcccttgctactttctaggcct-taattat--aatga-actttcagcgatctatgtgtgcccaaataaatttaactagtgaata

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ36878 (Selaginella moellendorffii), 5'ss of exon 4
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattct-gtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat
  | || |||||||| || ||||||||  | || |     |  || ||  | |||||||| | ||||||||||||| |||||||||||||||| || || |||||     || |   |||   ||| ||   |      | | | | ||| |                                                 
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGCCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagc---tgcctgggatttgagtagctt--actttgttctctcgctatag-------------------------------------------------

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ33528 (Selaginella moellendorffii), 5'ss of exon 3
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattct-gtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat
  | || |||||||| || ||||||||  | || |     || || ||  | |||||||| | ||||||||||||| |||||||||||||||| || || |||||     || |   |||   ||| ||   |      | | | | ||| |                                                 
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGTCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagc---tgcctgggatttgagtagctt--actttgttctctcgctatag-------------------------------------------------

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|162165067|gb|FC341621.1|FC341621
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|67709974|gb|BJ965790.1|BJ965790
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGG
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGG
EST: gi|162275529|gb|FC451284.1|FC451284
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|208374139|gb|DC952570.1|DC952570
EST:     GCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: GCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|100353954|gb|BY983394.1|BY983394
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGA
EST: gi|100384304|gb|BY969435.1|BY969435
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGGCCGATCACCAGC
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGG-CCGATCACCAGC
EST: gi|100386503|gb|BY951299.1|BY951299
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|162260011|gb|FC435314.1|FC435314
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|100361737|gb|BY947797.1|BY947797
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGGTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
EST: gi|162163441|gb|FC339975.1|FC339975
EST:     TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCT                         GGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA
genomic: TACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcac ... ttgtatgcagGGTATCCCGGAATCAGCTGAGATGCGACCTGTTGGGGGCCGATCACCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattctgtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG