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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtttagaatggagtcagcgcgaagcactgtacttccacacggctatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG

Basic information

species Physcomitrella patens
transcript PP1S56_243V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g47660.1 (Oryza sativa), 3'ss of exon 2
----gtgtttagaatggagtcagcgcgaagcactgtacttccacacggcta-tctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
    |   | |    |   |   |  |      |||   |   |     || |   |   || |  ||   | |     || |  | |  ||      | |||||||||||||||||||||||| ||||||||||||||    |||||||  | || || ||||| |||
gtgagccgtcatctcgtcattttcttgcgattttgtgggttttcttttttagttcatcttatctcgtgcggtttgctgatt-ggggcgc-ttgcccggtgtgcagGTACTTCCTGAGGAAGCTGAAGAAGGTGAAGAAGAGCAACGGCCAGATGCTCGCCATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g49030.1 (Oryza sativa), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcactgtactt--ccacacggctatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
          ||| ||| ||  |||    | |   |     |  |    |  ||  |||||  |  |   | ||   |||       ||| ||     ||||||||||||||||||||||| ||||||||||||||    | || ||  | || || ||||| |||
--------gttggtgtc-gcaagaactcttatctatgatgccttgatccttcgtgtaatttcgttgatgatttcgtgttg-------tttgtttgcgcgcagGTACTTCCTGAGGAAGCTGAAGAAGGTGAAGAAGAGCAATGGACAGATGCTCGCCATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G022619_T01 (Zea mays), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcact---gtacttccac-acggctatctgtacaattttttgta----atctctcagtttgaagtgaattttttcctt---tgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
              ||||| ||    |||    |  |||   | | |  | ||||     ||||||        | | || |   |  | |  ||  || |||   ||||||||||||||||| |||||| ||||||||||||||    | |||||  | || || ||||| |||
--------------gtcagtgccgtacaccctggggcttatgctaggattctctgattgtttttttccgttgcgtatttctgacggtggcgtcttgcttgcttgcgtgcagGTACTTCCTGAGAAAGCTGAAGAAGGTGAAGAAGAGCAATGGCCAGATGCTCGCCATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G022619_T02 (Zea mays), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcactgt---acttccac-acggctatctgtacaattttttgta----atctctcagtttgaagtgaattttttcctt---tgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG------------------------------------
              ||||| ||    |||  |    |||   | | |  | ||||     ||||||        | | || |   |  | |  ||  || |||   ||||||||||||||||| |||||| ||||||||||||||    | |||||  | || || ||||| |||                                    
--------------gtcagtgccgtacaccctggggcttatgctaggattctctgattgtttttttccgttgcgtatttctgacggtggcgtcttgcttgcttgcgtgcagGTACTTCCTGAGAAAGCTGAAGAAGGTGAAGAAGAGCAATGGCCAGATGCTCGCCATCAACGAGGTACAACCAATCCTTCACCCTCGTACCGTGAACGTT

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G113720_T01 (Zea mays), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcactgtacttccacacggctatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
        | || | |   | |   |  |  | ||  ||   | ||   ||     |  || ||| |      | | |        ||  |     |||||||||||||||| |||||  ||||||||||||||    | |||||  | ||||| ||||| |||
-----gtcagtgcattacacactcgggccgatgctagcat-tgtctgattgcgttttggttcgtatttctgacggtggcgtctcgcttgattgcgcgcagGTACTTCCTGAGAAAGCTCAAGAAGGTGAAGAAGAGCAATGGCCAGATGCTTGCCATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 2
--gtgtttagaatggagtcagcgcgaagcactgtacttccacacggctatctgtacaatttt--ttgtaatctctcagtt--tgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
  | | |   |      || ||||    |  | |  ||||    |      |      | ||   ||  |    ||  ||  || | ||   || |   |  |||||||||||||||||||| || ||||||| ||||||    |||| ||  |||| || ||||| |||
gtgagctgccatctatatctgcgcttc-ctttatgtttcctgttgaaggatttcttcgtcttaggtgcgagtcgtcgattaatgtactgctgttatctgtgcgcagGTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcactgtacttccacacggct--atctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
                              ||   || |  ||  |  |||  |  |    |||  | | ||||   | ||  |   ||| || |  |  |||||||||||  | |||||  |||||||||||||| ||||||||||  |||| |||||||| |||
------------------------------gtgagtcgagtcgattggatcgatcgatccatttccattttctc---tcgatttacctttctttcactctagGTACTTCCTTCGCAAGCTCAAGAAGGTGAAGAAGTCTCACGGCCAGATCCTCGCTATCAACGAG

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ38689 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttagaatggagtcagcgcgaagcactgtacttccacacggctatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
                           | || | |         | |||  | ||  |||   |  ||||||  |||        ||| || |  |  |||||||||||  | |||||  |||||||||||||| ||||||||||  |||| |||||||| |||
------------------------gtgagtggagtcgattggatcgatcgatcca--tttccattttctctcgattt-----acctttctttcactctagGTACTTCCTTCGCAAGCTCAAGAAGGTGAAGAAGTCTCACGGCCAGATCCTCGCTATCAACGAG

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|208353060|gb|DC926083.1|DC926083
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37825472|gb|BJ583538.1|BJ583538
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|18346362|gb|BJ178405.1|BJ178405
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37847485|gb|BJ605493.1|BJ605493
EST:     ACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: ACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37838414|gb|BJ596422.1|BJ596422
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37852027|gb|BJ610035.1|BJ610035
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37846767|gb|BJ604775.1|BJ604775
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|18343070|gb|BJ175108.1|BJ175108
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37822224|gb|BJ580290.1|BJ580290
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|208364358|gb|DC950659.1|DC950659
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAGGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG
                                        ttttttcctttgc  CT-rich tract
      tacaattttttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttagaatggagtcagcgcgaagcactgtacttccacacggctatctgtacaattttttgtaatctctcagtttgaagtgaattttttcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCTTGCTATCAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG