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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaatccgttttatcttagttttcggccatttacatttgcctaggaataagtgtccgacttctatgcataattgggactcaagttattttattcacattctattatctcttgcctcttcctcgctattcactagcctgacgcgcacgtttttatgtaatcaacag

Basic information

species Physcomitrella patens
transcript PP1S2_415V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_415V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA08G19320.2 (Glycine max), 5'ss of exon 3
GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaatccgttttatcttagttttcggccatttacatttgcctaggaataagtgtccgacttctatgcataattgggactcaagttattttattcacattctattatctcttgcctcttcctcgctattcactagcctgacgcgcacgtttttatgtaatcaacag
|||||||| |||||||||||||| ||||||||||| || |||| ||||||||| ||  | |||||  | ||||||||    || |   |  ||    |      ||          |||  | | |     |||  | ||   |||  |  ||       | ||| || |    |  | | |  |  |   |  |  |  |  | |                                       
GCTAAGACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGgt----tagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggcta--atggtttgttcctgtctatgttgttgtgcagaggtgcaagcactttgagattggtggtgacaag--------------------------------------

upper sequence: PP1S2_415V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA08G19320.1 (Glycine max), 5'ss of exon 3
GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaatccgttttatcttagttttcggccatttacatttgcctaggaataagtgtccgacttctatgcataattgggactcaagttattttattcacattctattatctcttgcctcttcctcgctattcactagcctgacgcgcacgtttttatgtaatcaacag
|||||||| |||||||||||||| ||||||||||| || |||| ||||||||| ||  | |||||  | ||||||||    || |   |  ||    |      ||          |||  | | |     |||  | ||   |||  |  ||       | ||| || |                                                                           
GCTAAGACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGgt----tagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggcta--atggtttgttcctgtctatgttgttgtgcag-----------------------------------------------------------------------

upper sequence: PP1S2_415V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA15G05670.1 (Glycine max), 5'ss of exon 3
GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgt---gatttaatccgttttatcttagttttcggccatttacatttgcctaggaataagtgtccgacttctatgcataattgggactcaagttattttattcacattctattatctcttgcctcttcctcgctattcactagcctgacgcgcacgtttttatgtaatcaacag
||||| || |||||||||||||| ||||||||||| || |||| ||||||||| ||  | |||||  | ||||||||    || |     |   |   |   |||| ||     |    |        |||   |||  |  | || |  ||  |  | |                                                                                        
GCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGgttagtatatggaaagcaatggatgcttttttggttccatgtggtgtgtggctaatggttgttag-ttcctgtctatgttgtgcag---------------------------------------------------------------------------------------

upper sequence: PP1S2_415V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 5'ss of exon 3
GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaatccgttttatcttagttttcggccatttacatttgcctaggaataagtgtccgacttctatgcataattgggactcaagttattttattcacattctattatctcttgcctcttcctcgctattcactagcctgacgcgcacgtttttatgtaatcaacag
|||||||| |||||||||||||| |||||| | ||||| |||| |||||| |||||  | || || || || ||||| |   | ||   || | || |   | |     | |     |||||            ||      | | || || ||  | |   ||| ||  | |    || |                                                                
GCTAAGACCACCAAGAAGATTGTTCTGAGGCTCCAGTGCCAGGGTTGCAAACACGTATCCCAGCACCCAATCAAGgtcag--agtc---ttaacctcaagctacacttttcttttcctgccttttgtgttacaccccttacttttacacaactga-atttttgttgttgcaattgggttttgcag------------------------------------------------------------

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|15261417|gb|BI436727.1|BI436727
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|162194481|gb|FC371121.1|FC371121
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|19790233|gb|BQ041766.1|BQ041766
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|18360544|gb|BJ192607.1|BJ192607
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|18369452|gb|BJ201539.1|BJ201539
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|6227524|gb|AW156123.1|AW156123
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|37838261|gb|BJ596269.1|BJ596269
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|18363955|gb|BJ196028.1|BJ196028
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|162230564|gb|FC407154.1|FC407154
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|162202251|gb|FC377587.1|FC377587
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
EST: gi|162195731|gb|FC371122.1|FC371122
EST:     TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG                         CGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA
genomic: TGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAA

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: 48

GCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAGgtgatttaat ... taatcaacagCGATGCAAGCACTTCGAGATTGGTGGAGACAAGAAGGGGAAAGGAACACAACTCTTTTAGATATAATGCTTTACTTTGTATTCCGAGAAATTATGAAGCA




<











<


<