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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgctgggtcatgattggggtttggtgggatagaagcgtcctccgccgcgcaactatgggcgcgtggcaggattgcaaccgatgggtggtgttg...

Basic information

species Physcomitrella patens
transcript PP1S69_31V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ15547 (Selaginella moellendorffii), 5'ss of exon 2
GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgctgggtcatgattggggtttggtgggatagaagcgtcctccgc-cgcgcaactatgggcgcgtggcaggattgcaaccgatgggtggtgttg---
||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||   | |   |    |   ||    ||     |    | || |       | | | |||    | |  |    |  |||| |      |   |  | |||   
GCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCCTCCGGATTATCCATTCAAGCCTCCAAAGgttcttgtagcgctagagattttccattccagtgctctgcagtgcttgaatcacactcaaactcgtgatctcatcgtgattcc--tttgttttttctcttgtag

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ27529 (Selaginella moellendorffii), 5'ss of exon 2
GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgctgggtcatgattggggtttggtgggatagaagc-gtcctccgccgcgcaactatgggcgcgtggcaggattgcaaccgatgggtggtgttg-
||| || ||||||||||| || || ||||| || || ||||| || ||||| |||||||||||||| |||||||| |||||||| |||||||| ||||||||| | ||  |       ||  |   ||| |  |     ||   |  ||  |    |   ||  |    ||       |||    |   | |||  |     
GCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAGgtatggcttttt--ctgggagcgatcttttgcagttcctaatttgctctttgtttggtctcttcgtcttcg-------attttttctttttggttctccaag

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ11261 (Selaginella moellendorffii), 5'ss of exon 2
GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgctgggtcatgattggggtttggtgggatagaagcgtcctccgccgcgcaactatgggcgcgtggcaggattgcaaccgatgggtggtgttg
||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||     ||  | | || |   |   ||   |   |  |    ||  | |      ||        | ||||     || |  |    ||  | ||    
GCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCCTCCGGATTATCCATTCAAGCCTCCAAAGgtt--cttgtagcgccagg---gactttccattccagtgctctgtagtgcttgaatcacactcaaactcgtgatctcatcgtgattcctgtcttgtag--

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ35297 (Selaginella moellendorffii), 5'ss of exon 2
GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgctgggtcatgattggggtttggtgggatagaagc-gtcctccgccgcgcaactatgggcgcgtggcaggattgcaaccgatgggtggtgttg-
||| || ||||||||||| || || ||||| || || ||||| || ||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||||| | ||  |       ||  |   ||| |  |     ||   |  ||  |    |   ||  |    ||       |||    ||  | |||  |     
GCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggctttt---ctgggagcgatcttttgcagttcctaatttgctctttgtttggtctcttcgtcttcg-------attttttccttttggttctccaag

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|162193815|gb|FC369223.1|FC369223
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208392917|gb|DC928603.1|DC928603
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|100444703|gb|BY982532.1|BY982532
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208368971|gb|DC955056.1|DC955056
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208354417|gb|DC953823.1|DC953823
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|100380283|gb|BY968931.1|BY968931
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208367859|gb|DC950940.1|DC950940
EST:     GATTATCCATTC-AGCCCCCCAAG                         G-TGCGTTCAGGACCAAGGTTTTCCACCCCCACATCAATAGTAATGGGAGC
genomic: GATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208386994|gb|DC956949.1|DC956949
EST:     GATTATCCATTC-AGNCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: GATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208353619|gb|DC946357.1|DC946357
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208366616|gb|DC955650.1|DC955650
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|37825009|gb|BJ583075.1|BJ583075
EST:     GATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: GATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208385507|gb|DC956677.1|DC956677
EST:     TATCCATTCNAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208370020|gb|DC948115.1|DC948115
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208390085|gb|DC942386.1|DC942386
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208398315|gb|DC920714.1|DC920714
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|18336116|gb|BJ168138.1|BJ168138
EST:     GATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: GATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|208358830|gb|DC957630.1|DC957630
EST:     CCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTNNNNNNNNAACATCNATAGTAATGGGAG
genomic: CCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTT-CCACCCCAACATCAATAGTAATGGGAG
EST: gi|18335330|gb|BJ167348.1|BJ167348
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
EST: gi|162193814|gb|FC369222.1|FC369222
EST:     TTCTGGTCACTATTCACTTNNNNNNNGATTATCCATTCAAGCCCCCCAAG                         GTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC
genomic: TTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGC

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: 31 (upstream exon), 35 (downstream exon)
Score: 111

GCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCCCCCCGATTATCCATTCAAGCCCCCCAAGgtaggtctgc ... gcggctgcagGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATAT




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