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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgattcaagctttgaagcagtgcttactggaaggtctgaattggatctttgatatcatggtgggagttttgtcttcacgtctggttttgagtcttgcaatatacaaagatgtgatctgtctcaatgttgcgtcgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 10
----------------------------gtattgatt--caagctttgaagcagtgct-tactggaag-gtctgaattggatctttgatatcatggtgggagttttgtcttcacgtctggttttgagtcttg---------caatatacaaagatgtgatctgtctcaatgttgcgtcgtgatg------cagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
                             |||  | |   |  |||| |    | ||    ||||||   | |  |    || |   || |  |  |     | |  | || |  |    | |  ||||||           | ||     | |  | |||||| |  ||||   | | | ||       ||||||||||| |||||||||||  |||| ||||| ||||| |||||||||
gtgcttttctatgttttctattcttgagttatcaaatgttacactttcacatggggcagctctggaattatttataactaatttaacattttttattttttttctcatattgatatagaatgtgaagtctttgtttatttttactaccttgatagcttatctgtgttgatgtgatggcattatattctttcagATTTATCCACCTATTAATGTCCTGCCATCTCTTTCACGATTGATGAAG
















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|208395424|gb|DC924478.1|DC924478
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|37837091|gb|BJ595099.1|BJ595099
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162153494|gb|FC329380.1|FC329380
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162278566|gb|FC454028.1|FC454028
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162230898|gb|FC406737.1|FC406737
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|67698241|gb|BJ958474.1|BJ958474
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162153495|gb|FC329381.1|FC329381
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162221565|gb|FC397582.1|FC397582
EST:     ACATCACCGAAGTTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG                         ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
genomic: ACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG

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), 11 (downstream exon)
Score: 2

ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAGgtattgattc ... cgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtcttgcaatatacaaagatgtgatctgtctcaatgttgcgtcgtgatgcagATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG
          aatatacaaa  TA-rich tract