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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttgataattatgttgtgttatatcaggctcttcgttgtctcaataatgcagggttgacaatcctcaatggaaagtacacttcacattttatacacgtcagacttgtttaatgctgtttgaaccttcctctttctctgttttcaagtctattctgacaatatcactatcgtgtgttgatgtacag

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_256V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G070422_T03 (Zea mays), 5'ss of exon 11
GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttgataattatg--ttgtgttatatcaggctcttcgtt--gtctcaataatgcagggttgacaatcctcaa-tggaaagtacacttcacattttatacacgtcaga-cttgtttaatgctgtttgaaccttcctctttctctgttttcaagtctattctgacaatatcactatcgtgtgttgatgtacag
| ||  |    ||| |||| |||||||| ||||| ||||||||  | |||||  | ||||| | || ||||||||||||||| |||||||||   || ||| ||  |  | | |      | |||||  |  | ||    |||   || |  || |  |  | || ||| | |    |  | ||| | ||     || |  ||| ||  |  |||||| ||                                                                          
GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTGgtcagagttttgactcctccctttgttacttgtgacttgctgtttcatccccctatttgaaaggtggcaacctttttcttcacagtgctctcttttttcttaacaagtatgctcttgttgaacag-----------------------------------------------------------------------
















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|37845830|gb|BJ603838.1|BJ603838
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162169757|gb|FC345294.1|FC345294
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|37845305|gb|BJ603313.1|BJ603313
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162176593|gb|FC353062.1|FC353062
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67720249|gb|BJ970508.1|BJ970508
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67727192|gb|BJ977451.1|BJ977451
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162176348|gb|FC353533.1|FC353533
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|18334218|gb|BJ166234.1|BJ166234
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     GATCAACTACTCCTCTGNTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162171617|gb|FC347558.1|FC347558
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162181163|gb|FC357608.1|FC357608
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162170699|gb|FC346286.1|FC346286
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|37824766|gb|BJ582832.1|BJ582832
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|18335658|gb|BJ167678.1|BJ167678
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162223700|gb|FC399772.1|FC399772
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCT
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCT
EST: gi|162223699|gb|FC399771.1|FC399771
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162182767|gb|FC359514.1|FC359514
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|162167231|gb|FC342796.1|FC342796
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|18333553|gb|BJ165568.1|BJ165568
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67725967|gb|BJ976226.1|BJ976226
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67720690|gb|BJ970949.1|BJ970949
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|208375034|gb|DC944815.1|DC944815
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|37830091|gb|BJ588103.1|BJ588103
EST:     GATCAACTACTCCTCTGNTAATGCANCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
EST: gi|67720235|gb|BJ970494.1|BJ970494
EST:     GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG                         ATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG
genomic: GATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttga ... tgatgtacagATGATGTAGGACATGCAGCTGCATTCTTGTCATCACCATTGGCTAGTGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAGgtgaggttgataattatgttgtgttatatcaggctcttcgttgtctcaataatgcagggttgacaatcctcaatggaaagtacacttcacattttatacacgtcagacttgtttaatgctgtttgaaccttcctctttctctgttttcaagtctattctgacaatatcactatcgtgtgttgatgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG