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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG

Basic information

species Physcomitrella patens
transcript PP1S59_173V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                       |||| |  |   | | |||  |   |  || |||  |       |||    || |||||      |||    | | |   ||  || | |||  |||    | ||||||||||||||||||| || |||||||| || ||||| || || |||||||   | || |||||||| |||
-----------------------------------------------------------------------ctgt-tctgctagtatcattcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgt----gtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTG---ACGGGTACAATGAAAAG

upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 4
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                    | | |   |  ||   ||   | |    |     |||| | |  | ||    |||||   | | ||    ||  | | |   | ||  | |   |  |||     |||||||||||||||||||| || |||||||| || ||||| || || || |||| ||   | ||||||||||||
----------------------------------------------------------------tttaaattt---tatggcaaaatattctctttgaaaaattacattgattaaag---ggtgagcatttgtactgctggtctgctgctaatg--atttcaaactgtt----cagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAATTCTGAAG---GGTACAATGAGAAG

upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                    |  || | |||   | ||  ||      |  || | |  | ||  |  |   | |   ||  |||  || || |   || |  ||     | |   || ||    ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |||   |||| || |||||||||
--------------------------------------------------------------------atactttgtgcaattaaaaaatcacttggagttctaaattagtactcta-cagct--cttcatctttgactggatacatattttt-----ttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTG---ATGGATATAATGAGAAG

upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                        || ||    ||      ||  |  |     | || | |  ||  || |  | | | |   | |   |  || |  |    |   | | |    | ||    ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |   |||||| || |||||||||
------------------------------------------------------------------------tgcattta-atactttgtgcaattgaaaaatcacttagatttttaaatttttactct---tcatctttgactggatatgctaacatttttttttatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATAC---AGATGGATATAATGAGAAG

upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtgg---tcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtc----tgacatgtcgctg-cagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                                    |||    | ||   ||| ||| || |   |||      || || ||| || | |  ||  | |  |   | || |  |     ||| ||   | || ||||||||||| ||||| ||||| |||||||| ||||| || || |||||||| | || |   || |||||||||
------------------------------------------------------------------------------------aacttgttaagaattttattatgttgagttctcgcctgtgatggtttggtgttattatacaactttcggactgtatttgctaatgatataaagttgacagACATTTGTAGGAACACCATTTTGGATGGCACCAGAAGTGATTCAGAACTCCGAAGGT---TATAATGAGAAG

upper sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 8
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                                                       ||     |  |||||| ||||         |||   |||    ||      | | ||  | | |  ||  |    ||||     | || |   |    |   ||||||||||| ||||| |||||||||||||| |||||||| || ||||| ||   ||| || || |||||||||
----------------------------------------------------------------------gctaggaaccaatgaac-atgtctaaaa---gttgaatggatcgaatgcctcttacttcatttcatgatatatatttttacactaatgtgtttaacaatg--acagACATTTGTAGGAACACCATTCTGGATGGCTCCAGAGGTAATTCAGAATTC---AGAAGGATATAATGAGAAG

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|100383755|gb|BY969284.1|BY969284
EST:     CAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG                         ACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCT
genomic: CAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAGgtcagttgac ... gtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
                                    gtctgac  putative branch site (score: 3)
                        atttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG