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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC

Basic information

species Physcomitrella patens
transcript PP1S33_110V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 1
cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatac-taaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-----
|| | | | | | | || || || || | | | | | |||| | | || | | |||||| || || |||||| || ||| | |||||||||||||| |||||||||||||||||||||||||| || || ||||| | |||||||| |||| | ||||
--gatatgtgtaatcttgttagctaaatcataattttcgtatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtttctatag----aaagATGGCGTCTCACATTGTTGGATACCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCCTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCTGAGGATT

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 1
---cggacacgcttgtccagaattttcttg--tgatgcat--tgatggtgcggatac---taaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
| | | | | | ||| || || | | ||| | | || | || | | | | | | |||| | | || | | |||||| || || |||||| || ||| | |||||||||||||| |||||||||||||||||||||||||| || || ||||| | |||||||| |||| | ||||
gttagcatatggatatgtgtaatcttgttagctaaatcataattttcgtatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtttctatag-

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os12g42884.2 (Oryza sativa), 3'ss of exon 1
--cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactca-tcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
||| | | | | | | || || || || || || | | ||| | | || | | |||||| || || |||||| || ||| | |||||||||||||| |||||||||||||||||||||||||| || || ||||| | |||||||| |||| | ||||
tatggatatgtgtaatcttgttagctaaatcataattttcgtatgtattcacatgacatttcgatgaatcaaactgatcgtagtacaattgtttctatag-

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 1
cggacacgcttgtccagaattttcttgt-gatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
| | ||| || | |||| | || | || | || | || || ||| || ||| |||| | ||| || |||||| |||||| |||||| | ||||||||||| || |||||||||||||||||||||||||| || || ||||| | |||||||| |||| | ||||
agcatgaccttaatcatatcgttctcatcaataaacatctgtattccttgttacaatagttga-catggtatttctgactgtaattctatttatggcacagAAA-GATGGCGTCCCACATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCACTTGAGTCTTTCTGGGATGGGAAGAGCACCGCTGAG

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G149751_T03 (Zea mays), 3'ss of exon 1
cggacacgcttgtccagaattttcttgt-gatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-----
||| || | |||| | || | || | || | || || ||| || ||| |||| | ||| || |||||| |||||| |||||| | ||||||||||| || |||||||||||||||||||||||||| || || ||||| | |||||||| |||| | ||||
----tgaccttaatcatatcgttctcatcaataaacatctgtattccttgttacaatagttga-catggtatttctgactgtaattctatttatggcacagaaa-gATGGCGTCCCACATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCACTTGAGTCTTTCTGGGATGGGAAGAGCACCGCTGAGGATC

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G112149_T02 (Zea mays), 3'ss of exon 1
cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-----
|||| | | ||| ||| | || | | | || | | | | |||| | | || | | || | | | ||||| |||||| ||||| | ||||||||||| || |||||||||||||||||||||||||| || | ||||| | |||||||| |||| | || |
tcttttagcttatttgcagctttgttgaggcaaatattcagc-tagcttctctatt-tctgtgaatca-acctgatcttaagattttactgttata-tagaaa-gATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAGGATT

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G112149_T01 (Zea mays), 3'ss of exon 1
cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactc-------atcagatatcttcctgtgtattcgtttctgcagca-gAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
||| | || || ||| || ||| || || ||| | | ||| | ||| | | | | | | | | || ||| | || |||||| ||||| | ||||||||||| || |||||||||||||||||||||||||| || | ||||| | |||||||| |||| | || |
-----gagctcttttag--cttatttgca--gctttgttgaggcaaatattcagctagcttctctatttctgtgaatcaacctgatcttaagattttactgttatatagAAAGATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAG

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 1
---cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
| ||| | || || ||| | || ||| | ||| | | ||| | ||| | | | | ||| | | | ||||| |||||| ||||| | ||||||||||| || |||||||||||||| ||||||||||| || | ||||| | |||||||| |||| | || |
gctagagagagctcttttag--cttatttgcagtttttttttgggacaaatattcagctagcttctctgtcaacctgatttta-acatttttctgttatatagAAA-GATGGCGTCCCATATTGTTGGATACCCTCGCATGGGCCCCAAGAGAGAGCTCAAGTTTGCCTTGGAGTCTTTCTGGGATGGGAAGAGCAGCGCCGAT

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
--cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttc--tgcagcagAAACGA-TGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC
| | | | | | || | || ||| ||| || ||| | | | ||| || | | || | || | | ||| |||||| | |||| || ||| | |||||||||||||||||||| |||||||| ||||||||||||||||| ||||| | ||||||||||||| | || |
gttgcatgtgttaatgcgga-tattattgccatg-atctatgaattt--tgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG-

upper sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G29180.2 (Glycine max), 3'ss of exon 1
cggacacgcttgtcca-gaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgttt-ctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC-
| | || | | ||||| ||| ||| || | || | | | | || | ||| | | | || || | | ||| |||||| ||||| || ||| | |||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| | ||||||||||||| | || |
-tattgccatgatctatggattttgttgc-atgtgttattcgttttatttatggagagtggacaagtgagagctaatttggagttttgatctgttgcgacagAAA-AATGGCATCTCACATCGTTGGATACCCCCGCATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCGAG

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|18374087|gb|BJ205665.1|BJ205665
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67702889|gb|BJ963122.1|BJ963122
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67702197|gb|BJ962430.1|BJ962430
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18368888|gb|BJ200973.1|BJ200973
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|100362680|gb|BY947474.1|BY947474
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|100385352|gb|BY950944.1|BY950944
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67709987|gb|BJ965803.1|BJ965803
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAG                         AAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGgtacgtagcg ... tctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
EST: gi|18327480|gb|BJ159483.1|BJ159483
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67712939|gb|BJ966388.1|BJ966388
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18330968|gb|BJ162974.1|BJ162974
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAG                         AAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGgtacgtagcg ... tctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
EST: gi|100377958|gb|BY949608.1|BY949608
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18361838|gb|BJ193905.1|BJ193905
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18364414|gb|BJ196487.1|BJ196487
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|100384569|gb|BY987428.1|BY987428
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18350806|gb|BJ182857.1|BJ182857
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67718712|gb|BJ968971.1|BJ968971
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18362361|gb|BJ194431.1|BJ194431
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67702366|gb|BJ962599.1|BJ962599
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAG                         AAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGgtacgtagcg ... tctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
EST: gi|100401427|gb|BY990997.1|BY990997
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18374880|gb|BJ206458.1|BJ206458
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18373260|gb|BJ204862.1|BJ204862
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|67719247|gb|BJ969506.1|BJ969506
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|100386286|gb|BY987953.1|BY987953
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18328770|gb|BJ160775.1|BJ160775
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|18332288|gb|BJ164301.1|BJ164301
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGCAG                       
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTT---CAGgtacgtagcg ... tctgcagc
EST: gi|100433344|gb|BY960558.1|BY960558
EST:     TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAG                         AAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG
genomic: TCGAGCTTCAGGCCTGTTTACTCAGGACAGGGCGTCTCTTCAGTCTTCAGgtacgtagcg ... tctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC
  tactaaa  putative branch site (score: 1)
 ttcgtttct  putative PPT
 taaactattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttctgcagcagAAACGATGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - -tgatgca