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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagattcatcattctattagatttctcatgaatattttaagtcgttaatgtatattgtaatccaaataccgagcttggattttgcttgaatttgtctctcaaatgaaaacttagcttcaaacataaatttatgcctggtaaagaggataacaaactgaagtttctcttgcaattttgtaatgcag

Basic information

species Physcomitrella patens
transcript PP1S204_118V6.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G176820_T01 (Zea mays), 5'ss of exon 2
GTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgta--cgagattcatcat-tctattagatttctcatgaatattttaagtcgttaatgtatattgtaatccaaataccgagcttggattttgcttgaatttgtctctcaaatgaaaacttagcttcaaacataaatttatgcctggtaaagaggataacaaactgaagtttctcttgcaattttgtaatgcag
  | || ||||||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || || || ||||| || ||||| || | ||||||    |||| | ||  | ||  |   | ||       |      ||    ||  ||| ||| ||  ||  ||| | |       | |||||||       | |  ||                                                                                    
TGCCAAGGGAGTCAACATCATGGCGTTCTGCAAGGAGTACAATGCCAAGACGGCCGACAAGCCCGGCTACATCATCCCCGTCGAGATCACCGTGTTTGATgtgagtgagactaatgctgtccgtcctactttgggcagaagcgagaatcgattgctgt-tatggttgtcataatgctggtt----actttgcttcg---cattttgcag-----------------------------------------------------------------------------------

upper sequence: PP1S204_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G32990.1 (Arabidopsis thaliana), 5'ss of exon 2
GTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagattcatcattctattagatttctcatgaatattttaagtcgttaatgtatattgtaatccaaataccgagcttggattttgcttgaatttgtctctcaaatgaaaacttagcttcaaacataaatttatgcctggtaaagaggataacaaactgaagtttctcttgcaattttgtaatgcag
 || || ||||| ||||||||||||||||||||||| || |||||||  || || || ||  |||||||||| ||||| ||||| ||||| || |  |||||  ||| ||  | | |||        |||  |  | || || |||  ||  |  ||    ||| | ||| |  |||      || || | | | |||  | |||||       |                                                                          
TTCTAAGGGAGTTAACATTATGGCTTTTTGCAAGGATTATAATGCAAGAACTGCTGATAAAGCTGGTTATATCATTCCTGTTGAAATCACTGTCTTCGATgt--gagttttgt-actct-------ctctactacaaatcttgagtttttgtttgat----taagctaaagaa-gagtaacatttgtggtggtaattggttatcaaaaatgtgtt--------------------------------------------------------------------------

upper sequence: PP1S204_118V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP06359 (Chlamydomonas reinhardtii), 5'ss of exon 3
GTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagattcatcattctattagatttctcatg----aatattttaagtcgttaatgtatattgtaatccaaataccgagcttgg--attttgcttgaatttgtctctcaaatgaaaacttagcttcaaacataaatttatgcctggtaaagaggataacaaactgaagtttctcttgcaattttgtaatgcag
       || || ||||||||||| ||||||||||||||||| ||  ||||| |  | | |  |||| | ||||||||||| || || || || || || || || || |       |||   |  |   | ||    ||    ||    |  |  | |    ||   |   |||  |   |  ||  |||| | ||||     |||                                                                                        
-------GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAGATGATTGGTGACATTATTCCCGTGGAGATTACCGTCTACGAGgtgcgcgact-gcagagctagcgggctctccctggcgaaaccccttgcacccctcctatgggctg-ggtatgaattgctcacacggctatttgggttgacgcaatctacag------------------------------------------------------------------------------------

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|16137669|gb|BI894533.1|BI894533
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|162219953|gb|FC396768.1|FC396768
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGAGATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|208352363|gb|DC902008.1|DC902008
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCANTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|162219952|gb|FC396767.1|FC396767
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGAGATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|162204417|gb|FC381645.1|FC381645
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGAGATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|162207263|gb|FC383300.1|FC383300
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGAGATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|208359431|gb|DC953984.1|DC953984
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
EST: gi|162207262|gb|FC383299.1|FC383299
EST:     CCGCAGACAAGCCTGGTTATATTATTCCCGTTGAGATCACAGTTTATGAT                         GACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA
genomic: CCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTA

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: 22 (upstream exon), 23 (downstream exon)
Score: 6

GTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAGACAAGCCTGGTTATATTATTCCCGTTGATATCACAGTTTATGATgtacgagatt ... tgtaatgcagGACAGAAGTTTCACGTTCATTTTGAAGACACCCCCAGCATCAGTTCTACTATTGAAAGCAGCTG




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