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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtag

Basic information

species Physcomitrella patens
transcript PP1S227_66V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 5
-GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacat-atgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtag
 |  |||||||| || ||||| ||||||||||| || ||||| ||||| || |||||| | |||||||||||  | | |  |     |||    | | |  | | |    ||||| |   | ||| || ||    | |   |     |  | |  | ||   | ||| |   | || |                                    
GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGAggt--tcgcttag-----tttaaccagtttttattttattatagtgaa--gtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacctgca-------------------------------

upper sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtag
|  |||||||| || ||||| ||||||||||| |||||||| ||||| || |||||| | || |||||||| |   |     ||      |||  | |  | |||   ||   ||||  |     |  |||||| | |       |  | |  | ||   | ||| |   ||    |||                                 
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaa---caagtttttttttattata--gtgaagcattgttcatttgtttgacagaagt----ttggttcctcctttgctaatttctctgttacctgcag--------------------------------
















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|162278618|gb|FC455016.1|FC455016
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|19790555|gb|BQ041934.1|BQ041934
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100388195|gb|BY951797.1|BY951797
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|208389895|gb|DC937726.1|DC937726
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGANGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCGCACTTGCAATGCTGGANCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|7286764|gb|AW599251.1|AW599251
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100413212|gb|BY956563.1|BY956563
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100364743|gb|BY947886.1|BY947886
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100362006|gb|BY947736.1|BY947736
EST:     AGTTTGCCATGTGGCTCTTGCGCNAGGAGG-CCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: AGTTTGCCATGTGGCTCTTGCGC-AGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|67718911|gb|BJ969170.1|BJ969170
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGANAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100384785|gb|BY950775.1|BY950775
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162172982|gb|FC347892.1|FC347892
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100442174|gb|BY963067.1|BY963067
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GGTCTCTTCGGCACAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAG
EST: gi|162158369|gb|FC334164.1|FC334164
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTGGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162199219|gb|FC375055.1|FC375055
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162258438|gb|FC434445.1|FC434445
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|208344467|gb|DC905028.1|DC905028
EST:     GAGTTTGCCATGTGGCTCTTGCGCANGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGANCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100410814|gb|BY956200.1|BY956200
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100353093|gb|BY945602.1|BY945602
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCNATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|208361763|gb|DC935003.1|DC935003
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGANGGCCATTGTCGCCCTGGAGAN                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162198077|gb|FC372104.1|FC372104
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|100390972|gb|BY952982.1|BY952982
EST:     GAGTTTGCCATGTGGCTCTGGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GT-CTCTTCGGCACAGAT-CCCACACTTGCAATGCT
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCT
EST: gi|100362852|gb|BY947561.1|BY947561
EST:     GAGTTTGCCATGTGGCTCTGGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCNATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162222838|gb|FC399300.1|FC399300
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|19780614|gb|BQ039583.1|BQ039583
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|162163969|gb|FC339879.1|FC339879
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
EST: gi|22492336|gb|BU052259.1|BU052259
EST:     GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG                         GTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG
genomic: GAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAG

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: 20

GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgtta ... atgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA