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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatttgctatttatgaatttatccagttatctatctttcagcaccttgccttctaaaaacggtagttgttgacatgttgttcttgaatggtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTG

Basic information

species Physcomitrella patens
transcript PP1S92_47V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os12g21798.1 (Oryza sativa), 3'ss of exon 2
caatttgctatttatgaatttatccagttatctatctttcagcaccttgccttctaa----aaacggtagttgttgacatgttgttcttgaatggtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTG
   |    ||||| |   ||||||    | |  || |||   || |  ||    |||    | |      ||| |||||| |  |  ||      |  | | ||||||| || || ||  | |||  |||||||||||||||||||||||||||| | || || || ||||| ||||| | ||| ||||| |  ||  | || |
tgttcctttatttgtctgtttatctgtgtttacatatttggtcatca-gcaacataatcttagatatcgtttgatgacatttgatattt---ccttcattttagATTGCTTCAGAGGGCCTCAAGCACCGTGTGTTTGAGGTCTCCTTGGCTGATCTTCAGAACGATGAGGATCAGGCGTACCGTAAGATCAGACTACGTGCCG
















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|67571386|gb|BJ944210.1|BJ944210
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|208360419|gb|DC950032.1|DC950032
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|19790465|gb|BQ041884.1|BQ041884
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|100450921|gb|CJ974507.1|CJ974507
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|37826206|gb|BJ584218.1|BJ584218
EST:     GGGAAAGACTCTTGTGACAAGGACTGCCGGCACCCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGA
genomic: GGGAAAGACTCTTGTGACAAGGACTGCCGGCA-CCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGA
EST: gi|18347427|gb|BJ179473.1|BJ179473
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|19777641|gb|BQ039208.1|BQ039208
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|18347038|gb|BJ179084.1|BJ179084
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|208372026|gb|DC936226.1|DC936226
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|162185712|gb|FC361566.1|FC361566
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|67694711|gb|BJ954944.1|BJ954944
EST:     AAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: AAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|6167400|gb|AW145664.1|AW145664
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|162261198|gb|FC437215.1|FC437215
EST:     GACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: GACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|100360481|gb|BY984147.1|BY984147
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|18345407|gb|BJ177450.1|BJ177450
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|18351838|gb|BJ183890.1|BJ183890
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|18371606|gb|BJ203208.1|BJ203208
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGANGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|18373995|gb|BJ205573.1|BJ205573
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|162216969|gb|FC393087.1|FC393087
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
EST: gi|19788665|gb|BQ040844.1|BQ040844
EST:     CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAG                         ATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT
genomic: CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgcca ... gtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgccttctaaaaacggtagttgttgacatgttgttcttgaatggtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTG
      ttctaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatttgctatttatgaatttatccagttatctatctttcagcaccttgccttctaaaaacggtagttgttgacatgttgttcttgaatggtggtatcagATTGCCTCCGATGGTTTGAAGGGCCGTGTGTTTGAGGTCTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA