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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag

Basic information

species Physcomitrella patens
transcript PP1S106_16V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S106_16V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G170602_T01 (Zea mays), 5'ss of exon 5
TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag
||| ||| || ||||||| ||    |||||||| || ||||| |||||||| ||| ||||||||||||| || ||||||||||| ||| | || | |||||| |    |         ||| |||      |||||| ||||| |     | | |||| |  | |   || |    |   |||| |  | |||   |     |   |  ||  |      |  |||||
TGTGTGGCACCCTCAGCCTGCGCCCAAGGACCACCCGTGGCGCTACATGCCCAACAACGCCATGACCCCTCACATCTCCGGCACCACCATTGATGGCCAGgtcagtgga---------catcagg------gtatcattcttagtagttagtagtgcagggctga--ggacg----acgactatgacgc-agatgtactaagcatgtttatggcatgggttggtgcag

upper sequence: PP1S106_16V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag
||| |||  | | ||||| ||   |||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || ||||| ||| | || || |||||  |  ||  | |       ||| | ||   |  |  | || |  |     ||| ||    ||    ||    | | ||  | |||   | |  || | |  |||                      
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttcta-----tagcactagcttgcccttttttacctaagttatttcac---ttggtggaacactaacattaagaat---aaaccaaacttgttcag---------------------

upper sequence: PP1S106_16V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA19G01200.1 (Glycine max), 5'ss of exon 5
TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag
||| |||  |   || || ||   |||||||||||| ||||| |||||||| ||||| |||||||| || ||||| || ||||| ||| | || || |||||  |   |        | || |  ||||    || || ||||  ||  ||  |   |||   | ||     ||| ||      ||  | |   || |  |    |  ||  | | ||  | || |||
TGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATTGATGCACAGgtattttcattaagtttctat-atcattatt-cattag-cttagctttttgtgtc-taagttctttctttcacttgatgg----aacactaattaattaattaatactaaaccatacttgtttttcag

upper sequence: PP1S106_16V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 5'ss of exon 5
TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag
||| ||| |  | ||||| ||    ||||||||||| ||||| |||||||| ||||| || |||||||| ||||| || ||||| ||| | || || |||||    ||   |  | ||  ||    ||    |  |  ||     ||  ||| || |      |   | |  | | | ||    |||    | | |||  |   ||                      
TGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCACCATTGATGCACAGgtacccaag--tttctacttttc---ttctccttcccttcccgtatttttgcttttctcatgcttgta-actcataaaatggccaat---gggacaatattgtgcag---------------------

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|208385885|gb|DC956723.1|DC956723
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|162269932|gb|FC445423.1|FC445423
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|18335876|gb|BJ167897.1|BJ167897
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|18341708|gb|BJ173743.1|BJ173743
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|208345467|gb|DC917350.1|DC917350
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|208386186|gb|DC949097.1|DC949097
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
EST: gi|67697753|gb|BJ957986.1|BJ957986
EST:     CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAG                         AAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC
genomic: CGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 37

TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaag ... cctcttgcagAAACGGTTCGCAGCCGGGACGAAGGACATGATCGACCGCTGGTTGAAGCACGAGGCTTTCCCCGAGCAGAACTACATTGTGCGTGAAGGCAAACTTGCGA




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