Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGCCCTTGATTTGCTTCCCCCTACACCCATGGTTTTGGATAACTGGAAGCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttctaatgagcatatgatttaatttagagcctcagtctgatactgagcacccatgcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccag

Basic information

species Physcomitrella patens
transcript PP1S172_22V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S172_22V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ26267 (Selaginella moellendorffii), 5'ss of exon 5
AACGCCCTTGATTTGCTTCCCCCTACACCCATGGTTTTGGATAACTGGAAGCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttctaatgagcatatgatttaatttagagcctcagtctgatactgagcacccatgcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccag
    | || || ||||| || || |  ||||||||||||||  |||||||| || | |||||||||||||||||||||||||||      |   ||  |   |    | | | ||      || ||  ||| |  || | |   || |  |    | |  | |   || ||                                                     
---CCTCTCGACTTGCTGCCACCGAGTCCCATGGTTTTGGACGACTGGAAGAGGCTCTACTCCAACACCAAGGCCAAGGACTTC---GCAGAAGTTGCTCTCAAAGgtacaagtgg-----tgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcag-----------------------------------------------------

upper sequence: PP1S172_22V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ14564 (Selaginella moellendorffii), 5'ss of exon 6
AACGCCCTTGATTTGCTTCCCCCTACACCCATGGTTTTGGATAACTGGAAGCGGTTGTACTCCAACACCAAGGCCAAGGACTTCC---ACTTGGCTATTAGTGgtacgtcttctaatgagcatatgatttaatttagagcctcagtctgatactgagcacccatgcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccag
    | || || ||||| || || |  ||||||||||||||  |||||||| || | |||||||||||||||||||||||||||    |  | ||| | |  |||||   |     ||     ||   |   || | |     |  |||||  ||| | |  ||  ||   |                                                       
---CCTCTCGACTTGCTGCCACCGAGTCCCATGGTTTTGGACGACTGGAAGAGGCTCTACTCCAACACCAAGGCCAAGGACTTCGCAGAAGTTGCTCTCAAAGgtacaagt---ggtgtttccattgatcgcttgaaa-----atgctgattttgatcccaaatctttgcag-------------------------------------------------------
















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|162219664|gb|FC395660.1|FC395660
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162174749|gb|FC352165.1|FC352165
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|208367120|gb|DC947826.1|DC947826
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162219663|gb|FC395659.1|FC395659
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37836307|gb|BJ594315.1|BJ594315
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATNGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37841558|gb|BJ599566.1|BJ599566
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTNGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|208368752|gb|DC955195.1|DC955195
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162152367|gb|FC328554.1|FC328554
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         CATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|208353736|gb|DC949770.1|DC949770
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|67726644|gb|BJ976903.1|BJ976903
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|208397891|gb|DC916646.1|DC916646
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37852199|gb|BJ610207.1|BJ610207
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|67692499|gb|BJ952732.1|BJ952732
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162162182|gb|FC337756.1|FC337756
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162162183|gb|FC337757.1|FC337757
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37835225|gb|BJ593237.1|BJ593237
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|67725191|gb|BJ975450.1|BJ975450
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|67725965|gb|BJ976224.1|BJ976224
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37850461|gb|BJ608469.1|BJ608469
EST:     AAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: AAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37826581|gb|BJ584593.1|BJ584593
EST:     CAAGGACTTCCACTNGGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: CAAGGACTTCCACT-TGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162229413|gb|FC405604.1|FC405604
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162152366|gb|FC328553.1|FC328553
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|162174748|gb|FC352164.1|FC352164
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|37847383|gb|BJ605391.1|BJ605391
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
EST: gi|18339267|gb|BJ171294.1|BJ171294
EST:     GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTG                         GATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT
genomic: GCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATT

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), 28 (downstream exon)
Score: 17

AACGCCCTTGATTTGCTTCCCCCTACACCCATGGTTTTGGATAACTGGAAGCGGTTGTACTCCAACACCAAGGCCAAGGACTTCCACTTGGCTATTAGTGgtacgtcttc ... aatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATTACAAGTACAATGATGAGAACCAAGTCACTTTCGTGACCATGAATAAGGT




<











<


<