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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA

Basic information

species Physcomitrella patens
transcript PP1S326_1V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 8
agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctt-------tttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
    || |     ||     | | |   ||| | || |   | | ||  ||||   || ||| |    |  |   |  || |  ||        | || |  | |||| ||  | || ||||  |  || ||| ||||  | ||||| |||||||| || ||||| |||| ||| ||||||||||| ||||||||||| ||||||||
---atctattttacttcagcttttc--aatgatctaatcatg-cattgcaataccattttagtttat-tggagttatcttataattgaaaaaactgttttattgcagACATCACAACGGCAGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
---agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
    || |    |  ||||         |||      || ||  |   |  || |   |  | |      |  || |    |       | ||| ||    ||||||  | |||||||  |  || ||| ||||  | || || |||||||| || ||||| |||| ||| ||||||||||| ||||||||||| ||||||||
agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatcttttttt---agATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 9
agtgtcaagagctctgagattgtgctgg--atgg---tttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
 |  |    || ||||         | |  ||||   | ||| |      |||  || |     ||  |||  ||    || |       | |||| ||    ||||||  |||| ||||  |  || ||| ||||  | || || |||||||| || ||||| |||| ||| ||||||||||| ||||||||||| ||||||||
ggaattgctagttctgtttcccccttagccatggaaatatatcattaatattt-gatgtacaaatacataggttcatctgactaacaaaatcttttttt----agATATAACTACCGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
--agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
    | |||  |    ||    ||   |   |  |||      |  |||||  ||| |   |   |    |  | |   ||    |||| |||   ||  |||| |   |||||| | || ||| || |||||| | ||||| || ||||| ||||||||||| | ||| |||||||| || |||||||| || ||||||||
actttctcactaaacatgcagctg-attatttcattttcccatgtgcttttc-tatagaaattattcatctgaatctgattaagtctttctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
--agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA-
  | ||  |   | |   ||||| | || |      | |  | |   | || ||       | | |    | |   ||   | ||      || || | |||||||    || |||   |  || | |||||| || || || || ||||| || ||||| || |  || ||||||||||||||||||||||| |||||||| 
ggaatggaactgggtagcagatt-tactagccctcctgtgcgtg-tttcttgatgaaacatttgtttttgttct-tgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
agtgtcaagagctctgagattgtgctggatggtttatta--gcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
| ||  |  || |   ||||| | || |      |  |    | |  | || ||   |   |   |    | |   ||   |  |      || || | |||||||    || |||   |  || | |||||| || || || || ||||| || ||||| || |  || ||||||||||||||||||||||| ||||||||
aatggaaccaggtagcagatt-tactagcccccctcctgttcctggttcttgatgaagcatttttttttgttct-tgatcatgagtaaacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------agtgtcaa---gagctctgagattgt-gctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
                         | |||      | |  | ||       | |  ||   || | | |     |||  ||  || | |   | | ||      ||  || || |||    |||  |||||| || || ||||     || ||||||||||| ||||| ||||||||||| || || || | ||| |||||||  |||||||||||||| ||||||||
gtacatccgactgctgatctgcactaatgtttgattgtgacccgattcaaccgttttataaattctgaacatttatttgttactgtac-aatcatcttcagtttcgtgctttctatttcgtctctgtagATATACCAACAGCAGCAATGGCCAAAGAAGCACTGGAAGGACACTGCATTTATGACGGTGGCTACTGTAAGCTTCGACTATCATACTCTCGTCATACTGA

upper sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 8
--------agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
        | |   |  | |   | || || | |||    ||||||     |   |   |    | || |  ||   | || ||  | ||| ||| ||||     ||||| |  | |||||||  |  || |||||||| || || || |||||||| || ||||| || |  || ||||||||||||||||||||||| ||||||||
tcaattttatttctaccaccatagggaatg-gttggcaattttatttatatctcatccctccactgctgggcaga--caaatgatctgttgttttctttc-----cagATGTCACAACTGCAGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA

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|162272186|gb|FC448695.1|FC448695
EST:     TGCAATTTTTGAGAAAAGTGCTGGTTTTCAAGCTTTGGTTCAATACCCAG                         ATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTT
genomic: TGCAATTTTTGAGAAAAGTGCTGGTTTTCAAGCTTTGGTTCAATACCCAGgtactataat ... tcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA
 ttttaat  putative branch site (score: 3)
                                tttttgctttttttct  putative PPT
                                tttttgcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT