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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttgttcgtcctttttacattcatgcagtgatttggtttggtcattagttgcgttgcaatatgagacttggcgacagcacttgacagttctttggatgtgtatttcccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAG

Basic information

species Physcomitrella patens
transcript PP1S400_36V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S400_36V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 1
gttttttgttcgtcctttttacattcatgcagtgatttggtttggtcattagttgcgttgcaatatgagacttggcgacagcacttgacagttctttggatgtgtatttcccatt-gcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAG
                       ||| |||    |||  |||   | |||| || | || |||| ||     || |||       | |   || |    ||   ||||    ||| | ||||| |||| | |   || ||||||||||| |||||||| |||||||| || |||||||||
----------------------gttc-tgctcc-attcagttgttttattaatttcttt-caatttggattgtgacgaa-----ctaatgattatgattattattattggttatttgtagTCACTTGAGACGGAGTATGGATGCAAGCTCTGCATTGGGCCTTGCACTACAAGAGGAGAG
















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|18364155|gb|BJ196228.1|BJ196228
EST:     CAAGGGTCGCGACACCTTCTGGCACTTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: CAAGGGTCGCGACACCTTCTGGCACT-CGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
EST: gi|100389829|gb|BY971181.1|BY971181
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
EST: gi|18373215|gb|BJ204817.1|BJ204817
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
EST: gi|18331447|gb|BJ163458.1|BJ163458
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
EST: gi|67572617|gb|BJ945441.1|BJ945441
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCA
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCA
EST: gi|18357116|gb|BJ189175.1|BJ189175
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACC
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACC
EST: gi|208391427|gb|DC937575.1|DC937575
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
EST: gi|67569369|gb|BJ942193.1|BJ942193
EST:     ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAG                         TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT
genomic: ACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACT

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: 26 (upstream exon), 24 (downstream exon)
Score: 4

GAGACCATTGGAGGGCGACTGCACTCTACAGTTACACAAATTTGAGTCAGACAAGGGTCGCGACACCTTCTGGCACTCGAGTGCTCACATTCTTGGCCAGgttttttgtt ... cccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagacttggcgacagcacttgacagttctttggatgtgtatttcccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAG
                  acttgac  putative branch site (score: 4)
                                          tttcccatt  putative PPT
                                      tgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttgttcgtcctttttacattcatgcagtgatttggtttggtcattagttgcgttgcaatatgagacttggcgacagcacttgacagttctttggatgtgtatttcccattgcagTCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA