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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttttgatatcatcattactagtttggctggtggcattcttatgcagtgctggatgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
----ttgtttttgatatcatcattactagtttggc--tggtggcattcttat-gcagtgctgg-atgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC
         |  ||   |||  ||  |  |||  |  | ||     | |||| |||  | |   |||| ||   | |     ||     ||   |    |||    |||| |||||| |||||||||||||| ||||||| |||||||| || || ||    || |||||  |||| ||||||||||| ||||| || || |||||||
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
-----------ttgttt-ttgatatcatcattactagtttggctggtggcattcttatgcagtgctggatgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC
            | ||  || ||| | ||| ||   |||   ||  |   | || ||    || |||  |||   | |||| ||      ||| |  ||    |  | | ||||||| || ||||||||||||||| | || || ||||||||||| || |||   ||||| || ||||| |||||||||||  | ||  |||| |||||||
aatgcagctagctattcatttataacctcagtat--gttactctatttagaatccta----gtcctgtttgaatcctctttgat------cttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
















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|162160963|gb|FC337494.1|FC337494
EST:     CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAG                         GTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
genomic: CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
EST: gi|162177600|gb|FC353186.1|FC353186
EST:     CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAG                         GTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
genomic: CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
EST: gi|162192128|gb|FC368277.1|FC368277
EST:     CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAG                         GTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
genomic: CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
EST: gi|162163792|gb|FC340339.1|FC340339
EST:     CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAG                         GTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
genomic: CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
EST: gi|162198258|gb|FC375509.1|FC375509
EST:     CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAG                         GTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT
genomic: CTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 35 (downstream exon)
Score: 9

GGCCAATAACTCACGGACTTGGAAGGAAGTGTGTTTCGCTTGTGTTGATGCTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttat ... gttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgctggatgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC
                    ctttaat  putative branch site (score: 9)
                                              ttttacc  putative PPT
                atcactttaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttttgatatcatcattactagtttggctggtggcattcttatgcagtgctggatgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - tgctgga