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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattgcggaagatcttatcgaagccttagctgcatttcacactgaaaatatcaacacatccgtttgttgtgggtgttgtttgaatcggatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG

Basic information

species Physcomitrella patens
transcript PP1S90_133V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
cttattgcggaagatcttatcgaagccttagctgcatttcacactgaa----aatatcaacacatccgtttgttgtgggtgttg-tttgaatcggatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG
  |   ||   |  ||     |      | | |  | | |  || |||      || |  |||||   | || | |   |  || | ||  || | |  ||||||||||||||||| || ||| | || ||||| || || || ||||| ||| | ||||   | ||||| ||||||||||| ||||| ||||||||||||   |
--tgacgctacatttccacctggtaggct-gttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgct--atgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

upper sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
cttattgcggaagatct-tatcgaagcct-tagctgcatttcacactgaaaatatcaacacatc-cgtttgttgtgggtgttgtttgaatcg--gatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG
     ||   ||| ||  |||  ||| || |      |    ||| |     |||  |   | | |     ||||   | ||  |||  |    | |      ||||||| || || || ||| | | ||| || || || ||| ||  | | || |||| | |||||||||| |||||||||||||| ||||| |||||||  |
-----tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

upper sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------cttattgcggaagatcttatcgaagccttagctgcatttc-----acactgaaaata---tcaacacatccgtttgttgtgggtgttgtttgaatcgg--atcaatgc-agGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG
                                                                                            ||||    || ||    |  ||||  |   | ||  ||     | ||   ||| |   |     |||   ||  |        ||||    ||  |   ||  ||  ||||||| || || || ||| | |  || || || || ||| ||  | | || |||| | |||||||||| |||||||||||||| ||||| |||||||  |
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatac-gtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

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|162169996|gb|FC345936.1|FC345936
EST:     TCAAACAGCTTTTAGGAGAGGCATCANAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCT
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCT
EST: gi|162217847|gb|FC393843.1|FC393843
EST:     TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
EST: gi|162201584|gb|FC377440.1|FC377440
EST:     TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
EST: gi|162186070|gb|FC361274.1|FC361274
EST:     TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
EST: gi|162178322|gb|FC354728.1|FC354728
EST:     TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
EST: gi|162188471|gb|FC365069.1|FC365069
EST:     TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAG                         GTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG
genomic: TCAAACAGCTTTTAGGAGAGGCATCAAAGAACATTCATATAATTTCGAAGgtgagtgtaa ... atcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaatatcaacacatccgtttgttgtgggtgttgtttgaatcggatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG
                                   tttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttattgcggaagatcttatcgaagccttagctgcatttcacactgaaaatatcaacacatccgtttgttgtgggtgttgtttgaatcggatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT