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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatattatccggagtatcttatcgtgaaaactctttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaatcaa...

Basic information

species Physcomitrella patens
transcript PP1S74_253V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACAC-TGGGgtaagatattatccggagtatcttatcgtga-aaactctttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaatcaa
                           |||  | |||||||| || ||||||||||| ||||||||||| ||||| ||| ||||||||||||  |  | |  |   | ||| |    | | | | |       ||  |   |  ||  |  | |||||   ||||     |||     | | ||||                
-------------------------ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtgccaatttcttaacattag---cgtgatgctttatttacag-------------

upper sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgta-agatattatccggagtatcttatcgtgaaaactctttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaatcaa
                           |||  | |||||||||||||| |||||||| ||||| ||||||||||||||| ||||||||||||  |  |  ||  | | || ||       ||    |  || ||||    | | |  |||   | ||   ||     || |      | | | ||                
-------------------------ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattactgtcatagagttatgcaaacaaact-tatgtgatgaatcctaa-cacgacctttg--atcctatatctacag-------------

upper sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 7
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatattatccggagtatcttatcgtgaaaactct-ttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaat-caa--------------------
                           |||| | |||||||| || || ||||||||||| ||||||||||| |||||| | ||  |  | |  |     || | || || |      | |       |   |  | | ||  || |  |||||   || |  |  | ||| |    |  | |     |    || || |||                    
-------------------------ATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTTgta----agtcaaatcttgtatttctttttggcctattctagttttgtttattgaactagttcacggaccatactctcgcactgctaagctatcagtaatagtgatacaagttcttatgtctggttacag

upper sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 7
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatattatccggagtatcttatcgtgaaaactctttctttaagatagtttctggtcattgatttcgtagaagtctgttta-tgtttcgggtaatcaa
                           |||  | |||||||| || ||||||||||| |||||||||||||| || ||||| || ||| | |  |      | |||||    |  | | || | |  ||   || | |    || |||||  | |    ||||  || | ||   ||   || | | || |   |      
-------------------------ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTATgtaagtttctcagatacacacgtgtgcat-tcagagttttaagt-tgaggttgagatacatgcaacacatt--ttgcatacttgtgcattcagtattgcatatg-----

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|208372471|gb|DC948725.1|DC948725
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|67727772|gb|BJ978031.1|BJ978031
EST:     CTCTGCGGGTGGTNCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: CTCTGCGGGTGGT-CCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|67696708|gb|BJ956941.1|BJ956941
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|162180521|gb|FC356163.1|FC356163
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|208361249|gb|DC957718.1|DC957718
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|208397278|gb|DC920632.1|DC920632
EST:     AAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: AAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|162184135|gb|FC358881.1|FC358881
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
EST: gi|162277008|gb|FC453106.1|FC453106
EST:     TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGG                         GTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC
genomic: TCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATC

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: 34 (upstream exon), 35 (downstream exon)
Score: 14

TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgtaagatatt ... ttttttgcagGTTCTGAACAAGTGGGAGCAGGTGCAGTCTTTCACTGCCTTCTCCAGCATCTACAACGACACTGGTCTCTTTGGTATCCATGCCACTTCTTCTGGTGACT




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