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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACACAATTTAAGTTTGAGCCCCTCCGCGATGATTTAGAATTCGGAAACTCGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccgctcactacaccgcgctcaggtttctcatctcgattgctcgatgtctgaattatctttctagagtgtcttgttaagtttctttttttcttctcaaattgaagccgctcgttgaattgtttgttgttttggcgcag

Basic information

species Physcomitrella patens
transcript PP1S36_62V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g09930.2 (Oryza sativa), 5'ss of exon 1
AACACAATTTAAGTTTGAGCCCCTCC---GCGATGATTTAGAATTCGGAAACTCGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccgctcactacaccgcgctcaggtttctcatctcgattgctcgatgtctgaattatctttctagagtgtcttgttaagtttctttttttcttctcaaattgaagccgctcgttgaattgtttgttgttttggcgcag
    |  |     |  || ||| |||    ||| ||    ||  |||| | |||  | |||||| | || ||  | ||||||||||||||||||||||| ||||||| |||  |   |  |  |     | |    ||   || | |||||       ||  || ||| |||    | | || || ||||    |||| ||||   |  || ||                                 
---CCGCTACCGCTGCGACCCCATCCCCGACGACGACCCCGAGCTCGGCACCTCCGCCTTCCCCGTCGTCCTCATCCAGATCCCCATGTTCAACGAGCGCGAGgtaccctctccctcccgccgccattgccgccaccttcccttgcttgctt------tgctttctctctctc---tttttttttgagttc---ttttgcttcgagatgtggagg--------------------------------

upper sequence: PP1S36_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G443715_T01 (Zea mays), 5'ss of exon 1
AACACAATTTAAGTTTGAGCCCCTCCGCGATGATTTAGAATTCG-GAAACTCGTCGTT--CCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctc-cgctcact------acaccg-cgctcaggtt---tctcatc-tcgattgctcgatgtctgaattatctttctagagtgtcttgttaag-------tttctttttttcttctcaaat-tgaagccgctcgttgaattgtttgttgttttggcgcag------------------------
    |  |    ||   ||||| ||||||| |     ||  ||| |     || ||    ||||||||| || || ||||||||||||||||||||||| |||||  |    |||   |       || ||| |||    |||   |||  || ||    | || | |  |  ||| |   | ||  |     |  || |       || | |    |   |  |  | ||    ||   | ||   || | | ||  | |  |||                         
---GCGGTACCGGTGGCAGCCCATCCGCGACGGCGACGACCTCGAGGCGGCCGCCGCCTACCCCATGGTGCTCGTCCAGATCCCCATGTTCAACGAGCGGGAGgtgagtgagcgcctgccggacggacgccggcgccggcgttggctctggtcgtctcgcgatcaaagcgttcatttttaatttaaggctagctagtaggggaggacttacatacactgaccgtacgtgtgcgtgcgtgtgctgggctgctggctggctggctgcatggtggtgcgtgcgtggacgtgcag

upper sequence: PP1S36_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G105631_T01 (Zea mays), 5'ss of exon 1
AACACAATTTAAGTTTGAGCCCCTCCGC---GATGATTTAGAATTCGGAAACTCGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccgctcactacaccgcgctcaggtttctcatctcgattgc----tcgatgtctgaattatctttctagagtgtcttgttaagtttctttttttcttctcaaattgaagccgct---cgttgaattgtttgttgttttggcgcag-----------
    |  |     |  || ||||||| |   || ||    ||  | ||   |||  |||||||| | || || || ||||||||||||||||||||||| ||||| ||  || | |    | ||||         |  || | | ||  |    | |  | |  |     | ||  || |  | |  |   | ||| ||   ||      ||     |  ||    || ||        |  |    ||||              
---CCGCTACCGCTGCGACCCCCTCCCCGAGGACGACCCGGAGCTGGGCTCCTCCGCGTTCCCCGTCGTGCTCGTCCAGATCCCCATGTTCAACGAGCGCGAGgtccgtacccccccgcccgccgccgcattacattgcagcgccatgccgccattgccggccaagcgcccgttgcagcggttttactccggattcgttgggtcactaataaccttggttgccttgcggtggtgccacgggcgggcgggcgtgcgttctctgcag

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|208348065|gb|DC905388.1|DC905388
EST:     CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
genomic: CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
EST: gi|67719482|gb|BJ969741.1|BJ969741
EST:     CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
genomic: CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
EST: gi|100368213|gb|BY948182.1|BY948182
EST:     GTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTTCA-CGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCA
genomic: GTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTT-CAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCA
EST: gi|100378886|gb|BY986466.1|BY986466
EST:     CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
genomic: CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
EST: gi|208346388|gb|DC912795.1|DC912795
EST:     CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
genomic: CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT
EST: gi|100443843|gb|BY982071.1|BY982071
EST:     CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAG                         GTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCTTGGCCAGGGGAT
genomic: CGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGAT

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: 12

AACACAATTTAAGTTTGAGCCCCTCCGCGATGATTTAGAATTCGGAAACTCGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccg ... tttggcgcagGTGTACCAACTCTCGATACAGGCAGCGTGTGGGCTGTCCTGGCCAGGGGATCGGATGATCATCCAAGTGCTTGATGATTCAACGGATCAGACTACAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACACAATTTAAGTTTGAGCCCCTCCGCGATGATTTAGAATTCGGAAACTCGTCGTTCCCCATGGTTCTGGTGCAGATCCCCATGTTCAACGAGCGAGAGgtacgctccgctcactacaccgcgctcaggtttctcatctcgattgctcgatgtctgaattatctttctagagtgtcttgttaagtttctttttttcttctcaaattgaagccgctcgttgaattgtttgttgttttggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT