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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttgtattttatggatcgtgttggttcattttgtagaatcgaatttgaagtggagcttcgttgtagtgatcaatgaaaatttctcttttaattaagtcagtctgtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG

Basic information

species Physcomitrella patens
transcript PP1S227_66V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatggttgtattttatggatcgtgttggttcattt-tgtagaatcgaatttgaagtggagcttcgttgtagtgatcaatgaaaatttctcttttaattaagtcagtctgtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG
        | | | | |  ||  || | ||| | || | |||     | | |   | |||   |   ||  ||  |  ||    || |     ||  || |  |        | || ||||||| ||||||||||||||||| || ||||||||||   ||||||||||    || ||  |  | ||   | |||  
--------gcagtctctaaat--tgatagtttacttatatagtgattactcttttg-ggattctatctggcgtccttcatctggatattgaacttgcttcaaac--------tttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
















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|162179912|gb|FC355983.1|FC355983
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|19790555|gb|BQ041934.1|BQ041934
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATC
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATC
EST: gi|100388195|gb|BY951797.1|BY951797
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162213332|gb|FC389620.1|FC389620
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|7286764|gb|AW599251.1|AW599251
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|100413212|gb|BY956563.1|BY956563
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162243293|gb|FC415642.1|FC415642
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162261369|gb|FC437802.1|FC437802
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162262854|gb|FC439273.1|FC439273
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162159195|gb|FC334366.1|FC334366
EST:     GCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: GCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162267272|gb|FC442060.1|FC442060
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162172982|gb|FC347892.1|FC347892
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162258438|gb|FC434445.1|FC434445
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|100410814|gb|BY956200.1|BY956200
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|67727259|gb|BJ977518.1|BJ977518
EST:     AGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAANTTACAGAGCGATGGAGTTT
genomic: AGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|19778198|gb|BQ039280.1|BQ039280
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACATAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|162222838|gb|FC399300.1|FC399300
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTT
EST: gi|19780614|gb|BQ039583.1|BQ039583
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTT
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTT
EST: gi|22492336|gb|BU052259.1|BU052259
EST:     TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG                         ATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCG
genomic: TCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCG

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: 35 (upstream exon), 35 (downstream exon)
Score: 30

GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAGgtatggttgt ... gtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgtagtgatcaatgaaaatttctcttttaattaagtcagtctgtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG
                           ttttaat  putative branch site (score: 30)
                                          tctgttt  putative PPT
          atcaatgaaaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttgtattttatggatcgtgttggttcattttgtagaatcgaatttgaagtggagcttcgttgtagtgatcaatgaaaatttctcttttaattaagtcagtctgtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA