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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcctcgcagttcagtttcagcgagtcgtatcgagtgatttgtgctggaaggccggttcatttctctactaggacctctgaagaagtgcatttag...

Basic information

species Physcomitrella patens
transcript PP1S101_218V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_218V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA14G03380.1 (Glycine max), 5'ss of exon 2
TGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcctcg--cagttcagtttcagcgagtcgtatcgagtgatttgtgctggaaggccggttcatttctctactagg-acctctgaagaagt--gcatttag------------------------------------------------
|||||||  |||| || || || |   || ||||   ||| |||  ||||||||||||| | ||||| || ||||| || || || ||||||||||| |||||||||  | |  ||  ||  |||||    || || |      ||| || ||          |  | | |  |  |    |  |||||| | ||  ||  |||                                                 
TGGTGGGAAGGGCTCTTCCTACCGAATCCGATGAGCATCCTAAGATCTACCGCATGAAACTCTGGGCCACCAACGAGGTCCGTGCCAAATCCAAGTTCTGgtatgtttattgttcatctctatttcaa-atgttgtttattcgtattcgtactaattcaataataaaatgcaatcttttctatttctgaaaacgttggccattaatcactttatagttattattattgacaatgtcaatgttaattgttacag

upper sequence: PP1S101_218V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv10s0003g03130.t01 (Vitis vinifera), 5'ss of exon 2
TGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcctcgcagttcagtttcagcgagtcgtatcgagtgatttgtgctggaaggccggttcatttctctactaggacctctgaagaagtgc-atttag
| |||||| | || |||||  | |  | | ||||   ||| |||  ||||||||||||  | ||||||||||| || || ||||| ||||||||||| ||||||||         |   | |     || | |||   | || ||  |  ||| |    ||||||  | |  | | |||  | ||      |   |  |||
TTGTGGGGAGAGCTCTCCCGTCGGAGAGCGATGAGCATCCGAAGATCTACCGCATGAAGCTCTGGGCGACGAATGAGGTTCGCGCCAAATCCAAGTTCTGgtatgtgggatatgataatgatgtctggatttgtagttattgtttgat--tggtaattgggttcaggttttgagttggagttttggtttgatctgaaatag
















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|162247160|gb|FC420228.1|FC420228
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCTAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|18326955|gb|BJ158956.1|BJ158956
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|37846860|gb|BJ604868.1|BJ604868
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|18334926|gb|BJ166944.1|BJ166944
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|18366480|gb|BJ198559.1|BJ198559
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|162210883|gb|FC387293.1|FC387293
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCTAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
EST: gi|162210988|gb|FC387294.1|FC387294
EST:     CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCTAAGTTTTG                         GTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT
genomic: CGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCT

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), 19 (downstream exon)
Score: 3

TGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCGCTAAATCCAAGTTTTGgtatgttcct ... tccttttcagGTACTTCTTGAGAAAGTTGCAGAAAGTAAAGAAGGCCCACGGACAACTTCTTGCTATCAATGAG




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