Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctacatattttgtgggatttaagattttaaaccaggttgataaatacatcccaaacagatgttcatatattggtcagcttacatcgaataaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3
AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctaca---tattttgtggg--atttaagattttaaacca-ggttgataaatacatcccaaacagatgttcatatattggtcagct-tacatcgaataaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag
 ||||| ||||| || |||||||| | |||  | ||||| |||||||||||| |||| ||||| |||||||||||| | |||||||| || |||||||||||  ||    ||| ||   |||||||| |   ||    ||| ||  |    | ||||   |||        ||  ||   ||| ||      || | |||||                                                                             
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagat--ggactaattcacatttagaccatagttgtacat-----------------------------------------------------------------------------

upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctacatattttgtgggatttaagattttaaaccaggttgataaatacatcccaaacagatgttcatatattggtcagcttacatcgaataaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag
 ||||  || || || ||||| || | |||  | |||||||||||||||||| |||| || || |||||||||||  | ||||||||||| |||||||||||  |    ||||   || ||  |   || |  ||    ||       |     |   ||     | | |  ||||||| |     |||  |        |||                                                                     
TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagtacttaataatatgtgtgagc--aatttgttatagccgagttattt--gataaagtttcatatgtgctcaagcccattctcctcaaat--------------------------------------------------------------------

upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G058138_T01 (Zea mays), 5'ss of exon 3
AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctacatattttgtgggatttaagattttaaaccaggttgataaatacatcccaaacagatgttcatatattggtcagcttacatcgaat-aaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag
 ||||  || || || ||||| || | |||  | |||||||||||||||||  |||| || || |||||||||||  | ||||||||||| |||||||||||           ||||  ||| | | | |||| || |   | ||  ||| || |  |   ||      |  ||  | |        ||  |  ||  || |||  ||                                                                 
TATGAAGAAAGCTGAAGCTGCGGGCAATGATAATTGTCCTGTGAAGATTAAACTAGTTGCTCCTCCACTTTATGTTCTGACCACACAGACCCTTGACAAGgttg---------acattattt-tagtacttaatatatgtgagcaatttgttatagccgagccttttgaagttttgtctgccctgaggcccatttctcatcaaatctgtg---------------------------------------------------------------

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|162237618|gb|FC413051.1|FC413051
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162236800|gb|FC413479.1|FC413479
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162217507|gb|FC393183.1|FC393183
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162236799|gb|FC413478.1|FC413478
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162223922|gb|FC398928.1|FC398928
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162202525|gb|FC380040.1|FC380040
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162206580|gb|FC382949.1|FC382949
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208351200|gb|DC921535.1|DC921535
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208345408|gb|DC917319.1|DC917319
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208372240|gb|DC948043.1|DC948043
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATCACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162189158|gb|FC365978.1|FC365978
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|67694015|gb|BJ954248.1|BJ954248
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208389139|gb|DC945715.1|DC945715
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|37832680|gb|BJ590692.1|BJ590692
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162259954|gb|FC435257.1|FC435257
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|6166827|gb|AW145091.1|AW145091
EST:     AGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162202498|gb|FC380039.1|FC380039
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162206579|gb|FC382948.1|FC382948
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCCCCACACAGACACTTGACAAG                         GGCCTGGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162163621|gb|FC339531.1|FC339531
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208353396|gb|DC946302.1|DC946302
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162223923|gb|FC398929.1|FC398929
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208386257|gb|DC952970.1|DC952970
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|208398568|gb|DC916089.1|DC916089
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162238555|gb|FC417410.1|FC417410
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
EST: gi|162237619|gb|FC413052.1|FC413052
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATNCAA-GCTTGTACGAAAGA
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTAT-CAAAGCTTGTACGAAAGA
EST: gi|37836440|gb|BJ594448.1|BJ594448
EST:     AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAG                         GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG
genomic: AGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAG

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), 34 (downstream exon)
Score: 23

AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaa ... tgcttgtcagGACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG




<











<


<