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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

Basic information

species Physcomitrella patens
transcript PP1S73_243V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
--gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgc-agCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
   |  | | ||   |  || |||  ||  |     || |  |||| ||| |  ||  | |  |||  |    ||   || || ||  | | |    ||| |||| ||||||||||| ||||||||||| |||||||| || ||||| |||||||||||  | ||||| || ||||| | |||| | || || ||  | ||||
gaattgaatgcttgctgaagttctgtatgcatgcaaacta-cattaccagaatctggcaccacttg--ctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
-------gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
          ||| |    |    |  || |||| ||||  |  |  | | | |  ||   |||  | |  |||  ||||  ||   |   | ||  | ||||  |||| ||||||||||| ||||||||||||||||| || || ||||| |||||||||||  | ||||| || ||||| | |||| | || || ||  | || |
atttgaacattatgtggttgctttgtgctgcatc-aaataaatgagcaattttatcagtgaatatagct--gacttggttacttg--tattgtttgttctgtt--agCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC

upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 5
--gtctattt--ctaagtacaggtc--tacatctaaatcgacaaata--ttatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
  ||  || |  ||  ||   | |   | || | | ||  |  |  |  ||| ||||   |      || | |   |    |||  ||||    ||||||  |   |||| ||||||||||| ||||||||||||||||| || || ||||| |||||||| ||  | ||||| || ||||| |  ||| | || || ||  | || |
aagttaatgtaactgggtttggtttggtgcacccagataaatgagcaatttaccagtgaatatagttgtctcggtaa---ctttgtattg----tttgttc-tgctagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAAACGCTTATTGCAGGTGGTCCTTTCGTGCTTCCCCTTGCACACAAAC

upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
gtctatttctaagtacaggtctacatctaaat-cgacaaatattatcagt-aggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
|| ||     |   | |   |   | ||||||  |  |    || ||||| |   || |||   |    ||    |   |        ||  ||||||  |||| |||||||| || || ||||| || ||||| || || ||||||||||||||||| ||||||||||||||||| | |||  | ||||| ||| ||||||
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcctctcattattttgtt--agCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 5
gtctatttctaagtacaggtctacatctaaat-cgacaaatattatcagt-aggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
|| ||     |   | | | |   | |||||   |  |   ||| ||| | |   || |||   |    ||    |   |        ||  ||| ||  |||| ||||||||||| || ||||| || ||| | || || || |||||||||||||| ||||||||||||||||| | |||  | ||||| ||| ||||||
gtttaagaacacagaaaagacactaactaaagatggtattcattgtcacttatcagacaacagatattagaaagctgaaatcctcttattattttatt--agCCAACAGTTGCTGCGATAGAAGCAGGGAAATACATAGCTTTAGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA16G10880.2 (Glycine max), 3'ss of exon 5
gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaat-tgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
 | | ||  ||  |      |||  |    || |   || ||  |    |  | |    |  || |  |   ||    ||   |  | || |||  | ||||| |||||||| || |||||||| || ||||| || || |||||||||||||||||  ||||||| ||||  || | |||  | ||||| ||| | || |
-tttcttcatagttctgctgctattttcgtattggtgaaaatcttagcaatattagttggcatgtattaaacttaaagatgctattggttattttcttcagCCAACAGTTGCAGCAATTGAAGCAGGGAAAGACATAGCATTGGCCAACAAAGAGACAATGATTGCGGGAGCCCCTTTTGTTCTTCCTCTTGCTCACAAAC

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|162155914|gb|FC332463.1|FC332463
EST:     CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA
genomic: CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA
EST: gi|162160113|gb|FC335983.1|FC335983
EST:     CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA
genomic: CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA
EST: gi|100377934|gb|BY949596.1|BY949596
EST:     AAGCCGTTACNNTGT-GT-ACANGAATTTGT-GGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGTA
genomic: AAGCCGTTAC--TGTTGTTACAGGAATT-GTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTA
EST: gi|208344624|gb|DC912570.1|DC912570
EST:     CANAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAN                         CCCACAGTTGCTGCTATTGAAGCTGGTAAA-ATATTGCCT
genomic: CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCT
EST: gi|19780903|gb|BQ039624.1|BQ039624
EST:     CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG                         CCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA
genomic: CAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAA

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: 31 (upstream exon), 33 (downstream exon)
Score: 24

GTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAGgtacgttcct ... tttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC
                                         tttgttt  CT-rich tract
                          ttttttaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC