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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
tttttgtttcaagcatgcaact-tctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                | | || |    ||| | ||     | ||   | |   |   || |    ||| | ||| |||      |||||  |||| | || | ||||| || ||||| ||||||||||||||||| || ||||||||||||||||||||||| ||  | || || || ||||||
----------------gtacctattatgagtccataggctttgttttcagacatgatgtgtaagatgaattgacatctac-----tgttt-tctgttc-agCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
-tttttgtttcaag--catgcaacttctca------agtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatc-atgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
 |   |  |   ||  ||||  | || | |      ||| | || |   |  |||    ||||  ||| ||  | ||  |  |  | |||||     ||  || |  ||| | ||||| || || || ||||||||||||||||| || |||||||| |||||||||||||| ||  | || || || ||||||
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctaccct-tcagacatg-atgtgcaagatgaat-tgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                |     | |    ||  || | |  ||| | |  |      |  ||| |  |  |     |    |  |||||   |    ||| | ||||| ||||||||||||||||||||||| || |||||||| ||||| || ||||| |||||  | || || || || |||
----------------gtctggttttgcttgtttactac--attgctattttttctgtttataagccatctta--ttggtgttttgtttcttt---tcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 13
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG-
                     |       |||||  |  | |    |  ||      ||  ||   | | |     |    | || ||      |   || | ||||| ||||||||||||||||||||||| || |||||||| || || || ||||| |||||  | || || || || ||| 
---------------------tctggttttgcctgcttaccacattgctattttttctgtttataaaccatctcattggtgttattttgtttcttttaagcTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
             |    | | | |   || | | |    ||||      || |      | |  ||   |     | |  | || |||   | |  ||| | ||||| |||||||| |||||||||||||| || |||||||| || || |||||||| |||||  | || || || || |||
-----------gtctctgatcatgttttgttcatcacagttatttt----tctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
    |  |  |   ||  |    || |  ||||||| |    | ||    |||   |    ||  ||| | |     |||||  | ||| |||    ||| | || || |||||||| || ||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||| || ||||||
---gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatata---gtatcgaattaattgacaacattctctttacct---tcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
-------tttttgtttcaagcat--gcaacttctcaagtgcctaatgcctattacgaaatcaggaatgga------tagg--gaacttacacctaacatcatgtttgcctg-tcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
       ||| | | |    |||   || | |  ||         ||  |||       | |    |  |      |||   || |||| || |   || ||||||   || |  ||||||||||| ||||| || ||||||||||| || || || ||||| || || |||||||| |||||| | ||||| || ||||||
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagctta-acttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaac-ttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                           |||   | |||        |   |||        | | | || |  || ||||    ||  || | | |  ||| | ||||| |||||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||  | ||||| || ||||||
-------------------------gtagtatttgatgttcgggctgcgttcaccttctctttgagcacgtcccaactaatgcgattctt-cttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcat--gtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
          |||  |   |   || |||||  |  |   | ||    | |    | ||  |   |  ||   | |  ||    |   |||  |     ||| | ||||| |||||||| |||||||||||||| || |||||||| ||||| || |||||||||||  | ||||| || ||||||
--------gtaagattcagaaggcttaagtgtgtttttaattttctccatt--atattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                                           |  |  ||   |  |  ||    |  |  |   |||||   | |     | |  ||| | ||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||| |||||  |||| || |||||||||
------------------------------------------gtgagcgattgtgtctacatcatta--tgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 12
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                                           |  |  ||   |  |  ||    |  |  |   |||||   | |     | |  ||| | ||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||| |||||  |||| || |||||||||
------------------------------------------gtgagcgattgtgtctacatcatta--tgccgtttaacaatgtctactggttttgcagCTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

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|208395424|gb|DC924478.1|DC924478
EST:     CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|37837091|gb|BJ595099.1|BJ595099
EST:     CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162153494|gb|FC329380.1|FC329380
EST:     CTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162278566|gb|FC454028.1|FC454028
EST:     CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162230898|gb|FC406737.1|FC406737
EST:     CTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|67698241|gb|BJ958474.1|BJ958474
EST:     CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162269042|gb|FC445534.1|FC445534
EST:     AAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: AAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162153495|gb|FC329381.1|FC329381
EST:     CTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162221565|gb|FC397582.1|FC397582
EST:     CTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     CTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG                         TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC
genomic: CTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAGgtgcgtatca ... cctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
                            acctaac  putative branch site (score: 2)
                                             cctgtccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA