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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA

Basic information

species Physcomitrella patens
transcript PP1S13_410V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_410V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDO97033 (Chlamydomonas reinhardtii), 3'ss of exon 1
---ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA
     | | |  |     | |   |  |      |  |  | ||   |     |      ||     | |||  |||  ||  |||   |  | |   || |||||| ||||| || |||||||||||  | || |  |||||||| || || || |||||||||||| | || || |||||||| || ||||||||||||||
agccagagctcagaggcgacgcccagctcgacatgagtgggaatacgtgcaacttcaaatggaagcgacgctgattt--ttggcttgggctgtgcac-tgcagATGGCAAGACCTTCAAGAAGCCCCGGCGTCCTTATGAGAAGGAGCGCCTGGACGCTGAGCTGAAGCTTGTCGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S13_410V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11758 (Selaginella moellendorffii), 3'ss of exon 1
ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA
                                        ||  |  |  || | | |  ||     | ||    |  |||   |           | ||||||||| || || |||||||| ||  |||| ||||||||||| || || || || ||||| ||| ||||||| |||||||| || ||||||||||||||
-----------------------------------gtaagtctctccttctc-gatcgcattgcgcccgtgccgatcgatccggtgtgcc------gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S13_410V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ31761 (Selaginella moellendorffii), 3'ss of exon 1
ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA
                                             |  |    | |  |   |     | |   |  |     |||   |  |   | ||||||||| || || |||||||| ||  |||| ||||||||||| || || || || ||||| ||| ||||||| |||||||| ||||| |||||||| ||
--------------------------------------------gtaagtctcgattcgcgctggcagtcgccgggatcatggatttggtggtgtcgcagATGGGAAAACTTTCAAGAAGCCGCGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGGCTCCGGAACAAGCGAGA

upper sequence: PP1S13_410V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ13465 (Selaginella moellendorffii), 3'ss of exon 1
ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA
                                        ||  |  |  || | | |  ||     | ||    |  |||   |           | ||||||||| || || |||||||| ||  |||| ||||||||||| || || || || ||||| ||| ||||||| |||||||| || ||||||||||||||
-----------------------------------gtaagtctctccttctc-gatcgcattgcgcccgtgccgatccatccggtgtgcc------gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

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|7067134|gb|AW496989.1|AW496989
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18344369|gb|BJ176409.1|BJ176409
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162232680|gb|FC409231.1|FC409231
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18339444|gb|BJ171471.1|BJ171471
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162267743|gb|FC443733.1|FC443733
EST:     CCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18326601|gb|BJ158600.1|BJ158600
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18351618|gb|BJ183670.1|BJ183670
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67720152|gb|BJ970411.1|BJ970411
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|19780475|gb|BQ039566.1|BQ039566
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18367844|gb|BJ199927.1|BJ199927
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67728167|gb|BJ978426.1|BJ978426
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         -TGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18342984|gb|BJ175020.1|BJ175020
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18360137|gb|BJ192199.1|BJ192199
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162276211|gb|FC452903.1|FC452903
EST:     CCGCAAGGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CCGCAA-GCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162250884|gb|FC426928.1|FC426928
EST:     CGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162200825|gb|FC377020.1|FC377020
EST:     CCGCAAGCTTCAACACCAAGATGGTGCACGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162224897|gb|FC401105.1|FC401105
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67573651|gb|BJ946475.1|BJ946475
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162267744|gb|FC443734.1|FC443734
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162242441|gb|FC416158.1|FC416158
EST:     CGCAAGCTTCAACACCAAGATGGTGCACGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67719905|gb|BJ970164.1|BJ970164
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         -TGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|7066992|gb|AW496847.1|AW496847
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67576093|gb|BJ948917.1|BJ948917
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162260272|gb|FC435575.1|FC435575
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|18346620|gb|BJ178665.1|BJ178665
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162260672|gb|FC436676.1|FC436676
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|37829233|gb|BJ587245.1|BJ587245
EST:     CAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|19779619|gb|BQ039455.1|BQ039455
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67717483|gb|BJ967742.1|BJ967742
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67701664|gb|BJ961897.1|BJ961897
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67697037|gb|BJ957270.1|BJ957270
EST:     TCCGCCAAGCTTCAACACCAAGATGGTGCACGNTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTTCGAGAAGGAACGTCTC
genomic: TCCG-CAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCC-TTCGAGAAGGAACGTCTC
EST: gi|37823568|gb|BJ581634.1|BJ581634
EST:     AAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: AAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|162241698|gb|FC417225.1|FC417225
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCATCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
EST: gi|67716955|gb|BJ967214.1|BJ967214
EST:     CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATT                         ATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG
genomic: CTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCG

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: 12

AGATCCTCTTTTCCAGTTTTTGTTCTCTTGCGGTGGAAGCTCCGCAAGCTTCAACACCAAGATGGTGCACGTTGCTTCCTTCCGCAATTgtaagtaatc ... ccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA
                      cttgtttgtttatctt  CT-rich tract
                          tttgtttatcttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgtttggttagaatgttaacattttagggtttacggatcgtttgtggtctggtaggtttttaggcttgtttgtttatcttattccttccttgtgtagATGGGAAGACATTTAAGAAGCCCCGTAGGCCCTTCGAGAAGGAACGTCTCGATGCTGAGCTGAAGTTGGTGGGAGAGTATGGTCTCCGCAACAAGCGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG