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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgtataaagtctcaactctatttcgtggttggtagatgctaatgtcagttttctactttgagtgtgtgcatgcgtgcacatgattctatatcttgatttaaagacatcgatgcctttgcag

Basic information

species Physcomitrella patens
transcript PP1S67_231V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_231V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 4
AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgtataaagtctcaactctatttcgtggttggtagatgctaatgtcagttttctact-ttgagtgtgtgcatgcgtgcacatgattctatatcttgatttaaagacatcgatgcctttgcag
| ||| ||  | || || |  ||||| || |||||  | || || || || |||||||||||||| ||||| || || |||||||| |||  |||||||||||||      || | |||     || |||   |||| ||   | || |||| |   | | | | ||||||  || ||   || | | | |||        | |||||                     
AAGGGAACCCTCAATTTTAGGTCTTTGAAATTCCGTGTCCTTGATGAGGCTGATGAGATGCTTAATATGGGCTTCGTTGATGATGTTGAGCTTATTCTTGgtatgcccacgtatattctagttgctcttt---ggtttgtgtgt-ctcatgtaatcatgccattgttgagttggtccaattgttctctttatt----ggtgttattta---------------------

upper sequence: PP1S67_231V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G164956_T02 (Zea mays), 5'ss of exon 4
AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgtataa-agtctcaactctatttcgtggttggtagatgctaatgtcagttttctactttgagtgtgtgcatgcgtgcacatgattctatatcttgatttaaagacatcgatgcctttgcag
|  || ||| | ||||||||||  || ||||||||  | || |||||||| |||||||||||||||||||| ||||| |||||||| |||   |||||||||||| |    |   ||| || | |  ||| |  ||||  || || | | | |   ||||  |   | | || || ||   | ||  |   || | | | |   ||                       
AAAGGAACTCTCAACTTGAAATGCTTGAAGTTCCGTGTCCTTGACGAAGCTGATGAGATGCTTAACATGGGCTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcacttgtcagtttctagt--attgca-ggttcttatatacaatttt---ttttacaacataaatgagtacaaatgagctaactgttttctttatacctt-----------------------

upper sequence: PP1S67_231V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G149520_T02 (Zea mays), 5'ss of exon 4
AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgtataaagtctcaactctatttcgtggttggtagatgctaatgtcagttttctactttgagtgtgtgcatgcgtgcacatgattctatatcttgatttaaagacatcgatgcctttgcag
|  || ||| | || |||||||  || || |||||  | || || ||||| ||||||||||| |||||||| ||||| |||||||| |||   |||||||||||| |  | |      |||  |    |   ||  | ||| || || ||  ||  |||||  |||||   | |  ||  ||   || ||  | ||   |   |||| |                   
AAAGGAACTCTCAATTTGAAATGCTTGAAATTCCGTGTCCTTGATGAAGCTGATGAGATGCTAAACATGGGTTTTGTTGATGATGTCGAGCTCATTCTTGgtatgctcatttg-----tcagtt----tctatgtattgtacattcttata-caaatttcttttttgacaatatagattagtatgcaggagccaattattatctttatac------------------

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|162195493|gb|FC369350.1|FC369350
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162173529|gb|FC350103.1|FC350103
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162203869|gb|FC379966.1|FC379966
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|100415313|gb|BY975254.1|BY975254
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162257462|gb|FC433323.1|FC433323
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCANAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162165696|gb|FC342263.1|FC342263
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162155569|gb|FC331013.1|FC331013
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
EST: gi|162254871|gb|FC430848.1|FC430848
EST:     CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTG                         GCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC
genomic: CGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACAC

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), 33 (downstream exon)
Score: 13

AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgt ... gcctttgcagGCGGTGTTGATGATCCCTCAAAGGTGCAAACTCTACTGTTCAGTGCGACACTACCCACTTGGGTTCAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGGCACTTTGAACTTGAAATCTTTAAAGTTCCGCATTCTCGACGAAGCCGATGAGATGCTTAACATGGGATTTGTGGATGATGTGGAGACTATTCTTGgtatgtttgtataaagtctcaactctatttcgtggttggtagatgctaatgtcagttttctactttgagtgtgtgcatgcgtgcacatgattctatatcttgatttaaagacatcgatgcctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA