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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S42_193V6.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagta---tgattcttagctcgtacttttaccaagtgcattatgtatgggt-cgtgcaacgaggt--aactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || ||||| |||||  | || || | |||||||||||||||  | ||  |||||||||| ||||||||  | || |||||||||||||| |||||   |    |||  | |    | ||  | ||  || | | ||| |  |  ||   |   | |   |  | | || || |  | | |||  ||      || || |||   ||             
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag-----------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA05G06110.1 (Glycine max), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || ||  | ||||| ||  |  | || || |||||||| ||||||||||||||||| ||||| || ||||| ||| | |||||||| ||  |  ||||||| |||| | ||||||     |  || ||     |  |||    |   ||     ||     |   |||||  | | | ||                                       
TATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGTCCATGGGTTACTTTGATATTCCTGTTGATCATGTACACTGTCAGgtaagta-ggttcttaa----tggttgtagtttatttattggtaacatgtttcctaatactattg-tttatgatgtccactag-------------------------------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 5'ss of exon 3
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 |||||||| ||||| ||  || |||| || |||||||||||||||||||| ||||| ||||| |||||||||||| | || || || || ||  | |||||         ||| |   |    | ||   |    |  | | ||||  | |||     | |   |||| |   |    | || |    |  || |||  | || |              
TATCACTGAAGCTGGTGCAGATCGAGTTCTTGCTTGTGATCTTCATTCAGGACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcac----ctctaaagccacgttcttgatac---ccctctttatgcattgtgtgt--atgctcctttgtgtataatacctttatctgc--ttaattg-tttcag--------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaag--tgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || || || ||  |||| || ||||||||||||||||||||||| || || ||||| |||||||||||  | || ||||| || ||| | |||||   | | | | | | |   |    |   ||||  |  | | | ||||   | |  ||  |  | ||   ||| |  |  | ||  |                                  
TATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAATCCATGGGTTATTTTGACATACCAGTGGATCATGTCTATTGCCAGgtatct-taagtttcaacctttttgatagacaagcctctactttttatgcaacctttaa-aatcttacacaattgtgattacatttcag---------------------------------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 || || || || || || ||  |||| || ||||||||||||||||| |||||||| ||||| |||||||| ||| | |||||||| || ||||| ||||| |  | |  |  |||||  || |  | | | ||| || ||     | |     |  || |  | |    |  || |   ||  |     |  |  | |  | || |            
CATTACAGAAGCGGGTGCAAACCGAGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCTATGGGTTATTTTGATATTCCAGTTGATCATGTGTATGGACAGgtaataagg--tgatagcttctagtggt-caatgtgtatgat---cagatttcaaactgatgctattggggttcttccatgttataca---tcagcatgactttggtgt-----------

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 5'ss of exon 4
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatgattcttagctcgtacttttaccaagtgcattatgtatgggtcgtgcaacgaggtaactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag
 |||||  | || || ||  |  | || || ||||||||||||||||| |||||||| ||||| || ||||| ||| | || |||||| | ||| ||||||| | ||  ||| |||   | |  ||| | |     | || | |      | |   ||    | |  ||| | |||    | || |                                  
TATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCCATGGGTTACTTTGATATTCCTGTGGATCACATATATTGTCAGgtaatta--atttttaagccattgtttgatccttatctttttctg-actccatatcactgaatgaaattactgtttgttttgtgcacacaag----------------------------

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|100383515|gb|BY950299.1|BY950299
EST:     CAGTNCA-TGGGATATTTTGACATTTCCGTTGATNCACGTT-ATGGGCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: CAGT-CAATGGGATATTTTGACATTTCCGTTGAT-CACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100356373|gb|BY946332.1|BY946332
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAAAACTCGACTACCTGGCAAGTAAA-TGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100399937|gb|BY990696.1|BY990696
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|162261958|gb|FC436817.1|FC436817
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTANAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100353033|gb|BY945573.1|BY945573
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCA-GTAAAATGATATCATCAAACGACTT
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTT
EST: gi|208380333|gb|DC907658.1|DC907658
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAACCGACTNG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
EST: gi|100372888|gb|BY948750.1|BY948750
EST:     GCAGTCAATGGGATATTTTGACATTTCCCGT-GATCACGTTTATGGTCAG                         CCTGGTA-TACTCGACTACCCTGGCA-GTAAA-TGATATCATCAAACGACT
genomic: GCAGTCAATGGGATATTTTGACATTTCC-GTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTG-TAATACTCGACTACC-TGGCAAGTAAAATGATATCATCAAACGACT
EST: gi|100353317|gb|BY964745.1|BY964745
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATC
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATC
EST: gi|162258694|gb|FC434389.1|FC434389
EST:     GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAG                         CCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG
genomic: GGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTG

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: 33 (upstream exon), 35 (downstream exon)
Score: 25

AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagtatga ... ttgtgtgcagCCTGTAATACTCGACTACCTGGCAAGTAAAATGATATCATCAAACGACTTGGTAGTGGTGTCACCAGATGTTGGGGGAGTAGCTCGTGCCCGTGCATTTG




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