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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG

Basic information

species Physcomitrella patens
transcript PP1S124_16V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttg-ggtatcacaatacacaagtgctgagatatgacgattgaact--tttctggg-acagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                                                             |  |  || |||| |     |   || | | |     | |   |    || || |||   ||||  ||    ||||     ||||||| || || ||||||||  ||| ||| ||| | || |||||  | ||| | |||||  | ||||||||||||||||| | |||||||||||| ||||
-----------------------------------------------------------------------------------------------------------gtaggtacagatgactactttcatactgtgatgttctgcttctgcaac-ttgcgaaatgctaattgccctagcgtctgctcgtagGTTGCCCGTGGTGATAAGACTGATGAAGACGGTGTGCCCATGCTGTTAAAAATCCCACGAATGTTTGATCCATGGGGTGGATTCAGTATCATTGGCTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttg-ggtatcacaatacacaagtgctgagatatgacgattgaacttttctg-ggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                                                        | | |   | ||   |      | ||  | | ||||||   |         | |     |||  | ||    | |||||   | ||||||| || || || |||||| | |  || ||| | || ||||| || ||| | || ||  | ||||||||||||||||| ||||| |||||||| ||||
-------------------------------------------------------------------------------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtt----tcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA11G02540.1 (Glycine max), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                                           | | |  |  | |     | |||| |   |  |     | | |  ||||        || | |  | |  | |     ||    ||       | |||| || || || |||   |     | ||| || ||||| ||| | || ||  | || ||| ||||||||||||||||||| ||||| ||||| |||||||
----------------------------------------------------------------------------------------gttagtattatgctctattctaattcatgacaatcactatcaccctatgtatt------tactaattttaatttttcttactt---tttactcaccatagGTAGCCCGAGGTGATCGAAGTGGAGAAGATGGAATTCCCATGTTACTGAAGTTCCCTCGTATTTTTGATCCATGGGGTGGTTACAGCATCATAGGTTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA01G42940.1 (Glycine max), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                                     ||   | ||||  | || |     | |||| |   |  |     | | |  ||||        || | |  | |  | ||   | |    ||       | |||| || || || |||   |     | ||| || ||||| ||| | || ||  | || ||  ||||||||||||||||||| ||||| ||||| |||||||
------------------------------------------------------------------------------------gttagtatatgttctattct-----aattcatgacaatcactatcaccctatgtatt------tactaattttaattt-tgcttactt--tttactcaccatagGTGGCCCGAGGCGATCGAAGTGGAGAAGATGGAATTCCCATGTTACTGAAGTTCCCTCGGATTTTTGATCCATGGGGTGGTTACAGCATCATAGGTTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 11
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatg-tcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                             |||||| ||| |  ||   ||  |  | ||  |  |||    | || |    |   || ||  ||| |  |      || |    | | |  |||    || ||    |||||| ||||| || |||||||     | ||| ||||| || |||||||| ||  | |||||||| |||||||| |||||||| ||||||||||| || ||||
----------------------------------------------------------------------------gtgagtgttttaaagaacaatcccccgtctctaccattc---ttcacaaagcttgattttggcctcata-catgatgctgttttcctgttaaaattattattctccat-acagGTAGCTCGAGGTGATAAGAGTGGAGAAGATGGTATCCCCATGCTTCTCAAGATACCACGTCTGTTTGATCCTTGGGGTGGTTACAGTATCATCGGATTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                  ||  | || |||| ||  |    |  ||      | | |||||  | ||  |||| ||| | | |  |  | ||| | |   ||   ||| | | ||             ||   ||  ||  |||| | ||   ||||| ||||| || |||| ||     | ||| ||||| |||||||| || ||  | |||||| | |||||||| |||||||| ||||| |||||||||||||
-------------------------------------------------gtgagt-gatttcttggaagatctcccttcgacaatatcacaaagcttgt--ttttgatctcataatac--atgattgatgcttttcttattaaacta-------------atgcaacattttcacttctttg---cagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCTTGGGGTGGTTACAGCATCATTGGTTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G01100.1 (Glycine max), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                             |||||| ||| |  || ||  ||  | | | || |     ||  | |  | |   || ||  ||| |  |      || |    | | |  |||    || ||    |||||| ||||| || |||||||     | ||| ||||| || |||||||| ||  | |||||||| |||||||| |||||||| ||||||||||| || ||||
----------------------------------------------------------------------------gtgagtgttttaaagaaagttctccctct-accatt-----cttcccaaagttgattttggcctcata-catgatgctgttttcctgttaaaattattattctccat-acagGTAGCTCGAGGTGATAAGAGTGGAGAAGATGGTATCCCCATGCTTCTCAAGATACCACGTCTATTTGATCCTTGGGGTGGTTACAGTATCATCGGATTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                  ||  | || ||| |||  |    |  ||      ||   || |   | | ||||| ||| | | || |  | |||     ||||     ||  | || || | |||         ||  ||  |||| | ||   ||||| ||||| || |||| ||     | ||| ||||| |||||||| || ||  | |||||| | |||||||| |||||||| ||||| |||||||||||||
-------------------------------------------------gtgagt-gatttcgaggaagatctcccttagactattcttcacaaagcttgttttttatctcataaaac--atgat-----gcttt----tcttattaaactaatgc--------aacattttcacttctttg---cagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCCTGGGGTGGTTACAGCATCATTGGTTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacga-----------ttgaac-ttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                                          || |   |  ||||||| | | |      ||| || | ||   ||| |   | |||   ||     | | |||  |  |           |||  | | || |   | |||| ||||| || ||||  |        || |||||||||||||| || ||  | || ||  | ||||||||||||||||| |||||||||||||| ||||
----------------------------------------------------------------------------------------gtaagtactgcttttttcacc-catatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG

upper sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcat-cacttcaa---gctgacgatcggtagcttgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                                                           | |   | ||   | |  |||   |      || || || ||   ||||| | | ||||  |  | | ||    | | ||| | | ||  ||||   ||||   |||    | | |||| ||||| || |||| ||     |  || |||||||| ||||| || ||  | || ||  | |||||||| |||||||||||||| |||||||| ||||
------------------------------------------------------------------------gtaagtagtttctccaaaacttgttagcccaccaatacatttgaaacggctgatgtttggtacttgagatctc-tgctgcccaattacagaattatg-taattgtgttttct--gtatagGTAGCTCGTGGTGATAGGAGTGGGGAGGATGGTATTCCGATGCTACTGAAGATCCCGCGAATGTTTGATCCTTGGGGTGGCTACAGCATCATTGGATTTG

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|37851091|gb|BJ609099.1|BJ609099
EST:     TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCANGATTGTG                         GTTGCTCGGGGAGATAAGNCCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|208363226|gb|DC954384.1|DC954384
EST:     TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTG                         GTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|37823707|gb|BJ581773.1|BJ581773
EST:     TTGATGAAAGCGTCATGATTGTG                         GTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|162174939|gb|FC350838.1|FC350838
EST:     TCTGGGTATTCATATCCCCGCTCATTTTTGATGANAGCGTCATGATTGTG                         GTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|100404116|gb|BY955263.1|BY955263
EST:     TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTG                         GTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|208398421|gb|DC916476.1|DC916476
EST:     TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTG                         GTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
EST: gi|208399425|gb|DC924855.1|DC924855
EST:     TCTGGGTATTCATATCCCCGCTCA-TTTTGATGAAAGCGTCATGATTGTG                         G-TGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA
genomic: TCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAA

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: 24 (upstream exon), 35 (downstream exon)
Score: 8

GTTTCTACTGTATTATTGAGTGCTGCCTTCATATACGATATATTCTGGGTATTCATATCCCCGCTCATTTTTGATGAAAGCGTCATGATTGTGgtatgttcat ... tctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtatcacaatacacaagtgctgagatatgacgattgaacttttctgggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTG
                                         cttttct  CT-rich tract
                                       aactttt  TA-rich tract