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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG

Basic information

species Physcomitrella patens
transcript PP1S105_42V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 7
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                                            |   ||  ||          || |||||||  |||       |   |||     || |  | |  ||||      |    | |   |||    |||       ||||| || ||||| || ||||||||||||||||| || || ||| | ||||| || || ||||| |||||||||||||| ||||| ||||| || || ||||
------------------------------------------------------------aatatttctttgctctacaactttacttgccttgttcttgttatcctatagttcatcttttgctactatatattcttgtataacaaaagaaactact------cagGTTGGTGACAATGTTGGAGATTGTGCTGCCCGAGGCGCTGATCTTTTTGAGAGCATAGCAGCAGAAATTATCAGTGCAATGATACTTGGAGGAACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                            || | |  ||| ||| |    || || | ||    ||| |  ||  | |           |||  |     | | |||| || ||||| |    | |  ||  |   | ||  ||     |||| || ||||| ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||
--------------------------------------------gtttataatttccttgacttgtgctttttgtt---tctttgtttatact-----------ttttctgg---tcttgtacttccattggtaccttactggttttaattt-tatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                               | |  || ||||  || || |||       | | |||||||    ||            | ||| | | ||| ||| ||  |||| |    | |  ||      |  |  ||     |||| || ||||| ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| || ||||||||||| |||||||| || ||||
----------------------------------------------atttccttgacttgtgcttttgtttc---tttgtttatactttttctgc-----------tcttatacagtta-tacttccgttggtaccttactggttttgattta-atttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgt-tggttctagtcctctctatacttgca-atgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcc---tgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                  | ||   | | |||     |||  | || |||   || ||| |   | || |||     |     || ||||     | || |||  | |    ||   |||  |     | | | || |   |   || |||||   |  |  ||   | |||| |||||||| ||||| || ||||||||  | ||||| ||||||||||||||||| || || ||||| |||||||| ||||| || ||||| || ||||
-----------------gtatttgatctttgt-----tctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                                                   ||  |||| || ||  | |  |     |    ||  ||||  |      |     | | | |   || |  || |       |    |  ||   |||||| |||||||| || || || || ||||| || ||||| ||||||||||||||||| || || ||||| |||||||| ||||| ||||| || || ||||
-------------------------------------------------------------------gtattagttctttcatttcacgatcctttgtgtatgattttgtcgggcctggaaccttttgtcatcactgaagcttc----actctcatcttcttgcagGTTGGAGACAATGTTGGGGACTGCGCTGCTCGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTTGGGGGTACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                                    |||  ||||  | ||  | |  || | ||| | | |    | || ||  |||      |||  | |      || ||    ||   |||| ||    | | | |||| ||  |||| |||||||| || || |||||||||||  | ||||| ||| | ||||||||||||||||||||||| |||||||| ||||| || ||||| || ||||
---------------------------------------------------atttgtttcattggtgcatttt-tcatgtctttgccttt--tttctaagggaa------aaatgtatgtcctttccataacaag---agtt-ttccctcttcttcatttga--agGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG

upper sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ13082 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                                                                                                                |||||| ||| || ||      ||  ||||  || |  ||  |   |    ||||| ||||| || || || ||||||||||| |||||||| |||||||| ||||||||||| || || || || || ||||||||||| || ||||| ||||
--------------------------------------------------------------------------------------------------------------gtaaattttgta-gtttac-----gtttagttgatgga--cttaatggtcttacagGTTGGAGATAATGTTGGTGATTGTGCTGCTCGTGGTGCTGATTTATTCGAAAGTATTGCTGCGGAGATAATTAGCGCCATGATTCTGGGAGGCACTATGG

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|162189733|gb|FC366787.1|FC366787
EST:     AAGGGATCCCTGAAGATGATGCAAGGAATCCTGCCGTAATTGCTGATCTG                         GTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAA
genomic: AAGGGATCCCTGAAGATGATGCAAGGAATCCTGCCGTAATTGCTGATCTGgtatgtgtaa ... attggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAA
EST: gi|162256270|gb|FC432176.1|FC432176
EST:     AAGGGATCCCTGAAGATGATGCAAGGAATCCTGCCGTAATTGCTGATCTG                         GTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAA
genomic: AAGGGATCCCTGAAGATGATGCAAGGAATCCTGCCGTAATTGCTGATCTGgtatgtgtaa ... attggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
                             ttattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG