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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttctttgcgaaacttaatcaggtgctatgttcatattgtctgcattcatcttttggagtatcatccttgatgtgccttatccattcaatagtt...

Basic information

species Physcomitrella patens
transcript PP1S169_73V6.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S169_73V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttctttgcgaaacttaatcaggtg-ctatgttcatattgtctgcattcatcttttggagtatcatccttgatgtgccttatccattcaatagtt---
  |  | ||  | || || ||||||||||| |||||||||||| | |||||||| || || ||| |||| || ||||||| ||  |||||| |  |   |  |  | |  |  ||||  |  | | |   || || |     | || ||         |   || | ||||  | | |    
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgt----aaatagcactggcatattatattgtgcattgtaaaatgctt

upper sequence: PP1S169_73V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 5'ss of exon 14
ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc--tttgcgaaacttaatcaggtgctatgttcatattgtctgcattcatcttttggagtatcatccttgatgtgccttatccattcaatagtt----------------------------------------------
  |    ||    || || ||||| |||||||| ||||||||| | || || |||||||||||||  || ||||||||||||||  |    |      | ||| |   ||  ||  | ||   | | | |||   ||   || | |   |    | ||||  |||| | |  |   |  |                                              
GAATGATTTTGTTTCTGCATCAGCTGACAACATCAAGAAGTTTAGCCTTCCTAAGGGAGAGTTTTGCCACAACATGCTgtaagttctagagtccttgtagttatttgagtctta-atccactctct-tacatct-tccagtgcaatgaaaaagataatgtttcttaactaaactggaaattttagttttctgatgtgttttcatgttatctttctttttggagcag
















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|162203186|gb|FC379283.1|FC379283
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|162175454|gb|FC350924.1|FC350924
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37832005|gb|BJ590017.1|BJ590017
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37822469|gb|BJ580535.1|BJ580535
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37823397|gb|BJ581463.1|BJ581463
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|162183680|gb|FC359908.1|FC359908
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|162198129|gb|FC373079.1|FC373079
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37827542|gb|BJ585554.1|BJ585554
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|18336709|gb|BJ168732.1|BJ168732
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37841942|gb|BJ599950.1|BJ599950
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37829602|gb|BJ587614.1|BJ587614
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37834715|gb|BJ592727.1|BJ592727
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37828539|gb|BJ586551.1|BJ586551
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|67720614|gb|BJ970873.1|BJ970873
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|162266558|gb|FC442789.1|FC442789
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|162160838|gb|FC337660.1|FC337660
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|208365406|gb|DC950873.1|DC950873
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
EST: gi|37823750|gb|BJ581816.1|BJ581816
EST:     AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT                         ATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT
genomic: AACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttc ... tcaaacacagATCTCAGCAGCGCACAATCGTTAATTGCATGTCTATCAACGAGGACAATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttctttgcgaaacttaatcaggtgctatgttcatattgtctgcattcatcttttggagtatcatccttgatgtgccttatccattcaatagtt

- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - -  AGAAGT