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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGAAGCCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactctcactcactctcgaccgatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc...

Basic information

species Physcomitrella patens
transcript PP1S45_97V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA04G00950.1 (Glycine max), 5'ss of exon 1
ATCGAAGCCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactctcactcactc----tcgaccgatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc
 |||  || |   |     |       ||||  |||| ||| |||||    ||||| || ||||||||| ||||||| |||||||| ||||||||||| ||||    ||  ||||| ||     ||  || |||    |||  ||       |||    ||   | |   |   |  |  | |      || ||   ||     
GTCGTCGCAGATCCACCAACCGTTATGGCTGCCTTCAGCGGTGATGAAACGGCTCCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtactc-cttccactctcttcaattcccccaatcacttccattagatccgtatttaccgtttcat-tatttatgtaatccgttcctaaaattgacttttaat--

upper sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 1
ATCGAAGCCGGCGCCATGTCGACCT---CTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgta--tggactctcactcactctcgacc-gatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc--
    || ||| || | |  |          |||   |||| ||| ||||||   || || || ||||||||| ||||||| |||||||| ||||||||||| ||||  |  |  |  | |   |||| |   |||||   |  | | |   | | |   | |||  | || ||| ||   |   |||  | |||  ||| ||  |   
---CAATCCGACGTCGTTGCAGTTATAATGGCTCCATTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatt--tctcaattagatctatgctcgtattttcttgatctcttttgaatttcactttatcaggaaattt--taatgt-tcgatgcgcaat

upper sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA11G11760.1 (Glycine max), 5'ss of exon 1
ATCGAAGCCGGCGCCATGTC---GACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgta--tggactctcactcactctcgacc-gatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttgg-ggtttggtgatggatcgttggacc
     | ||| || | | ||   ||     |||  ||||| ||| ||||||   || || || ||||||||| ||||||| |||||||| ||||||||||| ||||  |  |  |  | |   |||| |   |||||   |  |   |     | |   | |||  | || ||| |||  |    |||  || | |||   |     
---CCATCCGACGTCGTTTCAGTGATAATGGCTCCGTTCAGCGGCGATGAGACGGCACCGTTTTTCGGCTTCCTTGGAGCCGCAGCTGCCCTCGTCTTCTCCTgtaattcaatccctaatt--tctcaattagatctatgctcgtgttttcatgatctcttttgaatttcactttattaggataatttaatgttcgatacgtaat--

upper sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 5'ss of exon 1
ATCGAAGCCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactctcactcactctcgaccgatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc-
 |   | || |   |   |         ||   ||||  || ||||||  |||||| |||||||||||| |||| ||||| ||||| |||||||||||||||||   |    |  | ||||       ||   |       |   || || |||||    |||    | || ||| | | || |  | | ||    || | 
TTAAGATCCAGAATCGCCTGAGAGATGTCTACCTTCAGTGGCGATGAGACCGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccatctatactctcttataatctccatcttcttcttttctctttggttctgaattgttcactgatcttgtg-tgtgtttgttgttctcatgatct

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|208350047|gb|DC910282.1|DC910282
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|208400226|gb|DC908887.1|DC908887
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67507827|gb|BJ940704.1|BJ940704
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|100432293|gb|BY960411.1|BY960411
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|100352656|gb|BY945381.1|BY945381
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|19790121|gb|BQ041643.1|BQ041643
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|162206392|gb|FC383385.1|FC383385
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67718832|gb|BJ969091.1|BJ969091
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|100372520|gb|BY985638.1|BY985638
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67568945|gb|BJ941769.1|BJ941769
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|208355821|gb|DC930184.1|DC930184
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|208388958|gb|DC932986.1|DC932986
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|18354664|gb|BJ186722.1|BJ186722
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|208348535|gb|DC905814.1|DC905814
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|18351281|gb|BJ183333.1|BJ183333
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|100417075|gb|BY957154.1|BY957154
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|18354638|gb|BJ186696.1|BJ186696
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
EST: gi|67575975|gb|BJ948799.1|BJ948799
EST:     CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCAT                         GCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA
genomic: CGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCA

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: 35 (upstream exon), 35 (downstream exon)
Score: 59

ATCGAAGCCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactc ... ttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTACCAGTGGT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGAAGCCGGCGCCATGTCGACCTCTGCTGTGTTCAACGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATTGGAGCTGCAGCTGCTCTCGTCTTCTCATgtatggactctcactcactctcgaccgatctggcccagaagtggttcgtttgttcttgggtgtcgcttcattttggggtttggtgatggatcgttggacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT