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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG

Basic information

species Physcomitrella patens
transcript PP1S306_43V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 8
---gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
      || ||  || | ||    |     ||    ||||       |  |    |||       || | | | | |  ||   ||          ||||||||||||||||||||| || ||||| || |||||| ||||||||||||| |||
tttatggacattatgatttgatcaactcccagttaattgagacacttgctatct-gctgacaaaatattgttgatgtccactgggcccccccca--attgcagCCTTTGTTTCCTGGTGAAAGTGGTGTTGATCAACTGGTGGAAATCATAAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 8
---gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
    ||  || | |    |      | ||| ||       | ||    |  |    |  | ||  | |  |    |    |  | |||        ||||||||||||||||||||| || ||||| || || ||| |||||||||| || |||
atgcacattaggatttgatccgctcactgttgattgagacacttcttatccgatgacaatttggttgacatccact---gccccccttcccccaaaattgcagCCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgctt---ttgatg--ggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
    || || |||   |    || |||      ||    |             |||| | |    |||   |||| |     ||    |||| |  |  |||||||| ||||||||||||||||||||||| |||||  | || ||||||||||||
--gtatttggtgcaa-gaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
gacgatatgttgctgtggcgcaa-gtgtagaggtttg---aagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
    || || | || |     || |||   |  |||    |  |     |      | ||| ||| |  | | |  |||  |     ||    | |  |||||||| ||||||||||||||||||||||| |||||  | || ||||||||||||
--gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 8
gacgatatgttgctgtggcgcaagtgtagaggtttgaag---ttgaggtgagggagctttatgtgtaatctgggttt-tgacgacgcttttgatgggatt-gcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
   |  |||    | ||     | |       ||| |      |    ||       ||  || ||  | | | ||  |    |    | |  |   ||| |||||| |||||||||||||||||||| || ||||| || || || ||||| |||
---ggaatg--aatttgaaatgattcctatcttttaagacatcttccttgttcctatttactgggttttttagattgatagtaatctatgttgtattatttgcagCCATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 8
---gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
   ||  ||   || |||     ||    |      ||   |   |  |||   |  ||||  |  |  ||    | |||| | | || || |    ||||||||  ||||||| ||||||||||| || ||||||||||| || ||||| |||
taagataattccttcctggaagccactaattagctcttattgaataaatgacacatttttagattaatgcttatctatgactatg-ttgtgctat--ttgcagCCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 8
--gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG-
  ||  ||   || |||     ||    |   |  ||   |   |  |||   |  ||||  |  |  ||    | |||  | | || || |    ||||||||  ||||||| ||||||||||| || ||||||||||| || ||||| ||| 
aagataattccttcctggaagccactaattaggtcttattgaataaatgacacatttttagattgatgcttatctatgattatg-ttgtgctat--ttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 8
gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagcttta--tgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
              ||||      | | || | | |  ||||  |    | | ||  |  | |   | || | |||  |  | |  ||  ||     | |||||| |||||||||||||||||||||| |||||  | || || || ||||||
--------------gtgggtagtttattgatgctggtcgttgcagaagtgcatctaaaattcttggaacttgctttaaaatatgtcttccatttttgt-cagCCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAG

upper sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
gacgatatgttgctgtggcgcaagtgtaga-ggtttgaagttgaggtgagggagctttatgt---gtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
     ||   || |      ||  |||||  |  |||   | |   |     |  |  | ||   || || | || ||| |     |  |     ||  | |||||||||||||||||||| || ||||| |||||| | || || |||||||||
-gtagtacactgtta-atttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctgg--tacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG

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|100389546|gb|BY989024.1|BY989024
EST:     TAGATATATGGTCGATGGGTTGCGTGATGGCAGAGCTTCTACTAGGACAG                         CCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
genomic: TAGATATATGGTCGATGGGTTGCGTGATGGCAGAGCTTCTACTAGGACAGgtactcggtc ... gggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
EST: gi|67723790|gb|BJ974049.1|BJ974049
EST:     TGCGTGATGGCAGAGCTTNTACTAGGACAG                         CCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
genomic: TGCGTGATGGCAGAGCTTCTACTAGGACAGgtactcggtc ... gggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
EST: gi|100449000|gb|CJ973299.1|CJ973299
EST:     TAGATATATGGTCGATGGGTTGCGTGATGGCAGAGCTTCTACTAGGACAG                         CCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
genomic: TAGATATATGGTCGATGGGTTGCGTGATGGCAGAGCTTCTACTAGGACAGgtactcggtc ... gggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG
         tttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA