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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA

Basic information

species Physcomitrella patens
transcript PP1S174_37V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 6
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgt-tattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA
                                                  ||     || ||   |  || || | ||    |||||     | | |||   |      |  || |||| | |  |   || ||| ||  | |   ||   |  |||     ||    || || |||||||| || ||||||||||||||||| || || || |||||||| || || ||||| || || ||||||||    ||||| || |||   ||||| ||  |  
--------------------------------------------------gtgagtcttatttacataagtatcaggccgtcatgtgc----gaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattca---tgctt-ttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT

upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G27030.1 (Glycine max), 3'ss of exon 6
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttg-gatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA
                                                                     | |    | ||    | ||||| |   |||||| | |      || |   ||  | |||||   || | |   |    ||     ||   ||    ||||  ||||||||||| |||||| | |||||||||||||| || || |||||| | ||||| ||||| |||||||  ||| |   |||||| || | | | || || | | | |
---------------------------------------------------------------------gtaagtggtttatagtatgtatgtcatttgtctta-atactttgtaaggattgct-tggaagt-tgataattttggccttcttaattaaatgcat-atgtacttgttgcagCCTGACACAATCACAGGAGACATTGTTTTTGTATTGCAAGTAAAGGATCACCCAAAGTTCAGAAGGGAGCAGGATGACCTCTATATTGATCACAATCTCA

upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 5
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA
                                                                                                                 ||| ||||   | | |   |   |||| |  |        |   |       |||| || | |||||| |||||| | || || |||||  | ||||||||||||| ||||||||| || |||||||||||||| || || ||||| ||| ||||||| |   |  
----------------------------------------------------------------------------------------------------------------gtaa-gttagcttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctt-tggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT

upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ30223 (Selaginella moellendorffii), 3'ss of exon 5
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA
                                                                                                                 ||| ||||   | | |   |   |||| |  |        |   |       |||| || |||||||| |||||| | || || |||||  | ||||||||||||| ||||||||| || ||||||||||| || || || ||||| ||| ||||||| |   |  
----------------------------------------------------------------------------------------------------------------gtaa-gttagcttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctt-ttgcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGAAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT

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|162153711|gb|FC329114.1|FC329114
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAG
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAG
EST: gi|100431293|gb|BY960124.1|BY960124
EST:     ATGGCGCATGGGCAGAAGATTTACTTTTCCA-GGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: ATGGCGCATGGGCAGAAGATT-ACTTT-CCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|162151466|gb|FC326971.1|FC326971
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTG
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTG
EST: gi|162173994|gb|FC350509.1|FC350509
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|162161591|gb|FC338798.1|FC338798
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|162263312|gb|FC439094.1|FC439094
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTG
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTG
EST: gi|100441389|gb|BY962678.1|BY962678
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|162166513|gb|FC343210.1|FC343210
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|161979173|gb|EE296304.1|EE296304
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
EST: gi|100384322|gb|BY969453.1|BY969453
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCA-GGCGAAGCTGATGAGGCG                         CCCGA-ACAGTGCACAGG-GACCTTGTATTCGGTTTG
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTG-ACAGGAGACATTGTATTCGTTTTG
EST: gi|162234220|gb|FC409758.1|FC409758
EST:     GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCG                         CCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC
genomic: GCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 77

TCAGAAGGTGGTGCAGGATAAGAAAGTGTTGGAGGTTCATGTAGAGAAGGGCATGGCGCATGGGCAGAAGATTACTTTCCAAGGCGAGGCTGATGAGGCGgtgcgttact ... tttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA
        tgctgac  putative branch site (score: 77)
                 ttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA