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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtaatgtatcatagttggagcctttacatttgagaacatgtgagaaatctttagattgtattctagctttggagttattttcttcagttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG

Basic information

species Physcomitrella patens
transcript PP1S175_129V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S175_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 1
---------------------------------------acagtaatgtatcatagttggagcctttacatttgagaacatgtgagaaatctttagattgta-ttctagctttggagttattttcttcagttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG
                                          | || |   ||  |       || | ||   |||    |    |||||       | |||    | ||| |   | |     |   |    |   ||| | || |||||  | || ||  |    ||  |||||||  | ||||||||||| ||||||||||||||||| || ||||| |||
gtacacaatacgagccccgccgctaagattctcttgtatggggaaaaggcacaccgacttttgctatgcacgcgaggtgctcgccgaaatgccccagtggtaacattcgctgtctcgctgaaaacggtaccccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG
















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|100446650|gb|CJ970949.1|CJ970949
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|162231926|gb|FC408792.1|FC408792
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|100429680|gb|BY959684.1|BY959684
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|162223327|gb|FC400569.1|FC400569
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|18349218|gb|BJ181267.1|BJ181267
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|100437874|gb|BY961539.1|BY961539
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|100353475|gb|BY964825.1|BY964825
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
EST: gi|18357672|gb|BJ189731.1|BJ189731
EST:     GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAG                         ATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT
genomic: GCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGAT

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), 26 (downstream exon)
Score: 2

GGATGCACTCACAACAGTACCGCTGGCTACCAAGGGAGCCTCCTTTATCCGCAAGCACTTGCAGACTCTTGCACCCTATACTCCCATTGAGCCTTTTGAGgtatgttcct ... ttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatctttagattgtattctagctttggagttattttcttcagttatgtgcagATATTGTCTGCGAGACTAGGCAGGCACCCGAAGGACATTGTTAAGTTGGATGCCAATGAGAATCCATATGGACCGCCCCCTGAG
                                ttattttctt  TA-rich tract