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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT

Basic information

species Physcomitrella patens
transcript PP1S239_45V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------gtattgaaaactttcgtaaggtccactcccg-aaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                                                                  |||| | |||||   || |  ||   |   |  |||||| ||  || ||     |      |||||| | |       | || | ||||    | |   |||| ||||| ||||| ||||| || ||||||||||||||||| ||||| || || ||||||||||| ||||| || || || ||||| ||||| || || |
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtat-gtaaactgcagttacatcatttattgtgaaatgttact-tctttact--taatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------------------gtattgaaa-actttcgtaaggtccactcccgaaaatgtgaccgtcattggca----atggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                                                                       | ||||| | | || |    |         |  |  |     | | | | |    |||  |  || ||       |   || |  || |   | ||  | ||||| ||||| ||||||||||| || ||||||||||| ||||| || || || || ||||| ||||||||  | || || ||||| |||||||| || || |
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttg--ttgt-ctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------gtattgaaaactttcgta---aggtccactcccgaaaatgtgaccgtc-attggcaat---ggccagtacttttcctag---agatatttgattctaa----atcgtattcc--agGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                                            | ||| |  | ||  | |    |||  |        ||| | | | |  ||||   ||   |   ||   ||||  |||     || |||| || | |     | || |||   |||| ||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| || || || ||||||||||| || || |
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 4
---------------------------gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatc---------------------------------------------------------------------gtattc-cagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                                                                                                 ||| |                                                                     |||||| ||||| ||||| ||||||||||| |||||||||||||| ||||| || ||||| || ||||| ||||||||  | || ||||| || |||||||| |||||||
gtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 4
gtattgaaaactttcgtaaggtccac-tcccgaaaatgtgaccgtcatt---------ggcaatggccagtact---tttcctagag----atatttgattctaaatcgtattc-cagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
||||      |||  |     |  |  |  ||||||  |    ||||||          ||||     || |     |||  ||||      |||   ||  |      ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||| || || || || ||||| ||||||||  | || ||||| || |||||||| |||||||
gtatgtgttccttctggttatttaatattacgaaaactttcttgtcattttcttgcatagcaaaatttagcatgcaattttttagaatgttgtatggcatgtttgtgtatattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggcc-------agtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
      |  |     | ||  |||  |    ||||||| |   | ||  ||| | |||          |  |||| |||||  |  |   |  | |   |  |  |||| ||||| ||||||||||| |||||||||||||| ||||| || || || || || || || || || || || ||||| |||||||| || || || |
-----tatgatcactggaaattccgataatcaaaatgttatt-ttatctgcatttgccttcttaagagaactttcatagagtcaaattgctgcataatct-ctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                   | ||    |  |  | |  |  |   ||     |  ||  ||    || ||   |    || ||||| ||||| || |||||||| || ||||||||||| || || ||||| || || || ||| |||| ||||||||  |||| |||||||| |||||  |||
----------------------------------gtttgtttttgctctgaagggatcgaaacgaa--cgtgacttaaacaatactctgtt-cgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

upper sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                   | ||    |  |  | |  |  |   ||     |  ||  ||    || ||   |    |  ||||| ||||| || |||||||| || ||||||||||| || || ||||| || || || ||| |||| ||||||||  |||| |||||||| |||||  |||
----------------------------------gtttgtttttgctctgaagggatcgaaacgaa--cgtgacttaaacaatgctctgtt-cgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

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|162241445|gb|FC418584.1|FC418584
EST:     ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAG                         GTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
genomic: ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
EST: gi|162260898|gb|FC437955.1|FC437955
EST:     ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAG                         GTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
genomic: ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
EST: gi|162166033|gb|FC340429.1|FC340429
EST:     ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAG                         GTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
genomic: ACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
EST: gi|67507641|gb|BJ940521.1|BJ940521
EST:     GATGGGCATGAAG                         GTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
genomic: GATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
EST: gi|162182563|gb|FC357538.1|FC357538
EST:     TGGTGCTACAGAGATGGGCATGAAG                         GTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA
genomic: TGGTGCTACAGAGATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAA

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: 27 (upstream exon), 32 (downstream exon)
Score: 10

CAGCAAGGAGGCTATGATCTCTCTGCTTCGTAACGACTTCCCCGAGGCAAACGATTTTGGAAGTGAGGTCATTCCTGGTGCTACAGAGATGGGCATGAAGgtatgaattc ... cgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT
                                     ttctaaa  putative branch site (score: 10)
                             atatttgattctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaaaactttcgtaaggtccactcccgaaaatgtgaccgtcattggcaatggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC