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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaattgtagaaaaatcatcgatcgtgcag

Basic information

species Physcomitrella patens
transcript PP1S364_56V6.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 6
CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaat-tgtagaaaaatcatcgatcgtgcag
||||||||||||| || ||||||||||||||  |||| ||||||||||| |  ||||| ||||||||||||        |   ||||| |  ||   ||||| |        |||||  | |  |      | ||||   |  |   ||| |||||   | | |  | || ||                    
CTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAGgta--------tgtgcatctgtaccttgagaagtccattgtataagctaactgc--tggttgatgtttttttttattaccatctgattgtgaatgtgttatgcag--------------------

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G702426_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcat-----------ctc--tctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtga--------ttaaaagtctaattgtagaaaaatcatcgatcgtgcag-----------------------
||||||||||||| |||||||||||||||||  | || ||||||||||| |  || || |||||||||||| | | || | |||||           ||   | | | | ||   ||    ||  | ||| ||||||    |  |  ||    |||| |  | ||          || |   |||     |   || |  |||  || || |                        
CTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtatt-taacatgctcataaaaatgccaactagatattttctgagtatcttgcattgatctaatttcagagctgtattgttcttctggtacagaagtatccttccattttatgttctttccatttgaatagtatctgtc-tgtaatatatgtcatctttattttgtag

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G148744_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaattgtagaaaaatcatcgatcgtgcag
| ||||||||||| |||||||||||||||||  || | ||||||||||| |  || || |||||||||||| |   || |  |||||           ||   |    || ||  |  | |       ||| || || ||| |  || ||    || | || ||| || | |   |       || || || 
CCTACATGTCCTCACCTTGCCACATTGAGCTGATCTTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtattac-acatgttcatc----------aaatgccatctatatattttttct-------gagcatcttgcattggtctaat----ttcagag-ctatttttggcttaggttcttatggtaca-

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G127521_T01 (Zea mays), 5'ss of exon 5
--------------------------------CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaattgtagaaaaatcatcgatcgtgcag
                                ||||||||||||| || |||||||| |||||| || | || |||||||| |  ||||| ||||||||||||    |    ||   |   | | | |     | | |     || ||  ||| |||  |  | |||  |  | || ||  |||| | ||  || |  || |                      
AGCTTAACATTCTGTTTGCCTACCTGGTCCAGCTTACATGTCCTCCCCATGCCACATCGAGCTCATCTTGTCGGAGAAGGAAGAGCCAGTGAAGAAAGAGgta----tgtggacatgtggttgtgtacactgttgcacctgattacctgattt-agtgcatgggatta-atgttgtgctattgtggtcaatcgtttccttttcag-------------------

upper sequence: PP1S364_56V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G126594_T01 (Zea mays), 5'ss of exon 5
CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaattgtagaaaaatcatcgatcgtgcag
||||||||||||| || |||||||| |||||| || | || |||||||| |  ||||| |||||||||||| |||   | |      | | |   | |  |  |   | |    |  | ||||||  |  | |||  |  | || ||  |||| | ||  || |  || |                      
CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAGgta-tgtggac-atgtggttgtgtacactgttgcacttgatta---cctgattcagtgcatgggatta-atgttgtgctattgtggtcaatcgtttccttttcag-------------------

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|162192863|gb|FC370182.1|FC370182
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|7046864|gb|AW476808.1|AW476808
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|162271131|gb|FC447146.1|FC447146
EST:     GCCACATTGAGCTCGTCCTTTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|67721496|gb|BJ971755.1|BJ971755
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|18350729|gb|BJ182780.1|BJ182780
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37849723|gb|BJ607731.1|BJ607731
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|162239738|gb|FC417137.1|FC417137
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37830055|gb|BJ588067.1|BJ588067
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|162275627|gb|FC451642.1|FC451642
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|162265094|gb|FC440973.1|FC440973
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37832810|gb|BJ590822.1|BJ590822
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37851335|gb|BJ609343.1|BJ609343
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37836617|gb|BJ594625.1|BJ594625
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|13250457|gb|BG361360.1|BG361360
EST:     GCCACACTGAGCTCGTCCTCTCATAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGG
EST: gi|162239739|gb|FC417138.1|FC417138
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
EST: gi|37841405|gb|BJ599413.1|BJ599413
EST:     GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG                         GTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG
genomic: GCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttac ... gatcgtgcagGTTGAGGAAGTTGCTGCCCCCAGGACAAACAGGAAGAACCAAGCCCGCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAGgtaatgttacctactcatctctctctcccgaagttcgcaaatgtagctagtttcagtaaagagtattttacatggtcctcatgtgattaaaagtctaattgtagaaaaatcatcgatcgtgcag

- - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA