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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC

Basic information

species Physcomitrella patens
transcript PP1S59_133V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggt-------cgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                                                                                                    || | || || | |  | |  | | |     |  | |   |        |   |||    ||||| | ||||   | |       |  ||       |||||||||| || || ||| ||||||| ||||  ||||||||| |||| ||||| || |||||||  ||||| |||||||| |||||||| |||||||||||
---------------------------------------------------------------------------------------------------atgtgaaaggcctccttcatc-tgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g08440.2 (Oryza sativa), 3'ss of exon 1
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgc-gtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                                                                                             ||    ||  ||| ||||  |   ||||   |  | | ||| || |   ||      |    |   | ||        ||  | || ||  |  |  | ||| || |  || |||||| | |||||||| |  ||||||||  |||| || |||||||||||||  ||||| |||||||| |||||||| || || |||||
-------------------------------------------------------------------------------------------gtggcatagt-tgcattgcaacc--tgttgcaaggtatgctgctgttcttttgggagggtatcttgaatatgaatacgtgaacatcgttgctgcaattcatagGTATCTACATCATCAACCTCGGCAAGACATGGGAGAAGCTGCAGCTCGCGGCGAGGGTGATTGTTGCCATTGAGAACCCCCAGGACATCATTGTCCAGTC

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G126821_T01 (Zea mays), 3'ss of exon 1
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                                                                                             | ||| |      |||        ||  || |    | |   ||   |  ||      | |  | |        || | | | |   |     |   ||||||| |  || |||||| |||||||||| |  ||||| ||  ||||||| |||||||| || |  ||||||||||||||||||||||| ||||| |||||
-------------------------------------------------------------------------------------------cagcatgaggcttttatggggatctagtaattagctgtgatctatgg-agcact-tttagcagcttctccatcttcaagattcttgctactgtttttatcagGCATCTACATCATCAACCTTGGCAAGACATGGGAGAAACTGCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                                                                                     | | |   | || |  | |||  | | |||||    ||  || || | | |      | ||   |   |  ||||   |   |   |||        |   ||  ||||||| |  || |||||  |||||||||| |  || || ||  ||||||| |||||||| || |  ||||||||||||||||||||||| ||||| |||||
-------------------------------------------------------------------------------------tagct-gtgaattgtggagcaccgta-gcagc----ttaatagcgcttcatcttcaagatgaattgttgggtgtgatata-cattcatgctactttttttttgt-cagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G159237_T02 (Zea mays), 3'ss of exon 1
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgca-gcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcg-catcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                                                                                           | || | |  |  || |||   |  | |||| |  |   |     | |   | |   |   | ||| |||   | |||  | | |  ||  |||       |||| || |  ||||| ||| |||| |||||||  || |||||| || | || || ||||| || |  ||||| ||||| |||||||||||||||||||||||
------------------------------------------------------------------------------------------aatggctcgtagttcagtgctaactcgagttgcttatgctggcaatttcttatac---ctaacagta-gtgcttttgta-tattattatcatcattatctttcagGTATCTACATTATTAACCTTGGAAAGACCTGGGACAAGCTTCAGTTGGCCGCCAGGGTCATCGTTGCCATTGAGAATCCGCAGGACATTATCGTGCAGTC

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|208379664|gb|DC903719.1|DC903719
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|100429439|gb|BY959564.1|BY959564
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|18329684|gb|BJ161690.1|BJ161690
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|100403042|gb|BY973478.1|BY973478
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|100439438|gb|BY961933.1|BY961933
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|67716287|gb|BJ966547.1|BJ966547
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|162160077|gb|FC335947.1|FC335947
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|208399572|gb|DC908753.1|DC908753
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|162248750|gb|FC422822.1|FC422822
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|67569851|gb|BJ942675.1|BJ942675
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
EST: gi|18324853|gb|BJ156848.1|BJ156848
EST:     GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG
genomic: GAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTG

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: 30 (upstream exon), 32 (downstream exon)
Score: 6

GAGTCCGATGTGCAAATGATGCTGGCTGCCGATGTGCATCTCGGCACCAAGAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattc ... cggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC
                         tggtaac  putative branch site (score: 6)
                            taacaat  TA-rich tract