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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
        |  | |    |     | |  || |  | |||||         ||     ||   | | |  |  ||  ||     |||  |  || ||            ||||| |  |    |||| ||||| || || |||||||| |||||||| ||||| || || || ||||| || || |||||||||||||| ||||||||  | ||| | |||||| 
-------acacccgtggcccgtgcataatttcttttaattgaagtgcataatccgtgtatatgtcattgctataaaatgt----tgtctttggttttat----------cttgttgcct----agCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTTAGTGAGGGCACAAGTGCAGATCGTGAGATTCAGAGGACATTGATGGAGC

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtct-tgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
                                       |||| || |  || | ||  |   || || |         ||| ||  | | |   | | || |      |||| || |  ||  |||||||||| || |||||||||||||| ||||| |||||||| ||  | || || || || |||||||||||||| ||||||||  | || || |||||| 
--------------------------------------gtgag-atgcttgtgtgaaattgtcttcctataggtttacacatactaatttaaagatgttctaaatctatacttttcttgatt--agCCGTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgatt-actcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
                              |   || |||| ||      |||||   || | || || | |   |  || |   |||||| | |||     |||    |||||          |||| ||||| || |||||||||||||| ||||| |||||||| ||  | || || || || |||||||||||||| ||||||||  | || || |||||| 
-----------------------------gtgagataattgtgtgaaattgtcttcctataggtttacacatactaattgaaagatgttctaaatct-----atacattacttgat-------tagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgatt-actcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
                                        |   ||||  |  | ||  ||  || |    | |||   | ||   |||||||||||             | | | |||| |  |||| ||||| || |||||||||||||| ||||| ||||| || ||| | || || || || |||||||| ||||| ||||||||  | ||||| |||||||
----------------------------------------gtagattcttgaatgaagtttctttcatatattaaaatggaatatggttctgagtctc------------cattttgtttgttaagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGT

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0038g04350.t01 (Vitis vinifera), 3'ss of exon 6
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctga-gtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
                                       | ||| ||    |     ||| |  |  | |  |   ||| |  || | |  | |   | || || |     || | | || |  |||| || || || |||||||||||||||||||| ||||| || ||| | || ||||| || |||||||| ||||| || |||||  | |||||||||||||
--------------------------------------gtaagtgtttgaatt---gcatgggattttttcgatttgtgaaatctttgccaatgatattctaat-tactgttttttgcttgtcaagCCCTGTATCATTTTTATGGATGAGATTGATGCCATTGGTGGGCGTCGTTTCAGCGAGGGAACAAGTGCTGATCGTGAAATTCAGAGAACACTCATGGAGT

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|162266639|gb|FC441999.1|FC441999
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|37836411|gb|BJ594419.1|BJ594419
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|162269526|gb|FC445082.1|FC445082
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|37834916|gb|BJ592928.1|BJ592928
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|208353233|gb|DC926158.1|DC926158
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|37823384|gb|BJ581450.1|BJ581450
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
EST: gi|37833453|gb|BJ591465.1|BJ591465
EST:     AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAA                         CCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT
genomic: AAAGTGCGAGACTCATTAGAGAGATGTTTAGTTATGCTCGCGACCATCAAgtaattttct ... gtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
                          tgctgat  putative branch site (score: 3)
                                           tcgttttt  putative PPT
                                              ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgattactcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA