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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcatcccttcttcctgcccagtttgttgtgtggtggcgcagctccttgatgttctttgttgacctcgtttctggtggctgttgcag

Basic information

species Physcomitrella patens
transcript PP1S358_6V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 5'ss of exon 3
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcatcccttcttcctgcccagtttgttgtgtggt-ggcgcagctccttgatgttctttgt-tgacctcgtt-tctggtggct-gttgcag---
|||| |||||||| |||||||| ||||| ||||| ||||| | |||||| || |||||||| |||||  | ||||||||||||| ||| ||    |||||||||   |     | |||   | |||  | |  ||  |  |   |   ||| ||        ||| |  ||   |    | ||   | |  |||      
AAGCAGAGAAGGAATTTAGAGTCGAAGTTGAAGCCATCGGTCACGTTCGGCATAAGAATCTGGTGCGACTTCTGGGGTACTGTGTGGAAGGGATACACAGgtgatcatttcttcctctctgttccctttgttctgcataattaactttgctgctcagcccagtttatacgaatccaccatgtgcaagttcattgtgatac

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 5'ss of exon 2
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcatcc-cttcttcctgcccagtttgttgtgtggtggcgcagctccttgatgttctttgttgacctcgtttctggtggctgttgcag---------------------------------------
| ||||||| |||||| |  ||||| ||||| || ||||| ||||| || ||||||||||||||  | ||||| || ||||| |||||||| |||||| |||  |   ||  | |  |    |  |||  | |  |  |  |        || ||  | || || | ||  ||| |  | | |   |  | |                                         
AGGCGGAGAGGGAGTTCAAGGTGGAGGTGGAGGCAATCGGCCGCGTCCGCCACAAGAATCTCGTCAGGTTGCTCGGCTACTGCGCGGAGGGAGCTCACCGgtacactacacacaccacgcaattgccaaatcgccgccttctttttt--ttctttcctttttttggctgttctcttaccagatcattcctacctacctactccgatcctaccatttcttgcctgtgatctcag

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G317938_T01 (Zea mays), 5'ss of exon 2
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcat------cccttcttcctgcccagtttgttgtgtggtggcgcagctccttgatgttctttgttgacctcgtttctggtggct-gttgcag-------------------------------
| || ||||||||||| |  ||||| |||||||| ||||| || ||||| ||||| ||||||||  | ||||| || ||||| |  ||||||||| ||||||   |||  |      | | |     |  |   || |||  ||||   |  || | |||       |||   |  |||  |  |||  ||| | | | |                               
AGGCCGAGAAGGAGTTCAAGGTGGAGGTGGAAGCAATCGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTCGGCTACTGCGTAGAGGGTGCTTACAGgtatgtgtgttggcaggcacattgcaatctcttcttcgttcggtggacacctagttgcttctctcaatttagggttctcaatgatggaagcttgcttctgtatatcactactatggtctatgcttgaacag

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G01330.1 (Arabidopsis thaliana), 5'ss of exon 2
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcatcccttcttcctgcccagtttgttgtgtggt-ggcgcagctccttgatgttctttgttgacctcgtttctggtggctgttgcag
|||| ||||||||||||||||||||||||||||| ||||| || ||  | || |||||||||||  |  |  | || ||||| |  || || ||  |||||| |     |      |  | |||    |  |   | || | ||  |   |  |  |  ||  |   |     ||||| |||    |  |  ||
AAGCTGAGAAGGAGTTTAGAGTGGAAGTGGAAGCTATCGGGCGTGTAAGGCATAAGAATCTCGTTAGGCTATTAGGATACTGCGTCGAAGGAGCATACAGgtaagaaaaagaaacccg-catgcttgatacggactttgctcggtacttgttttgaactttgataagtcttaacgtttttgg-aattcctctag

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 5'ss of exon 2
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaat-gtcatcccttcttcct--gcccagtttgttgtgtggtggcgcagctccttgatgttctttgttga--cctcgtttctggtggctgt-tgcag----------------------------------------------------------------------------------------
|||| |||||||||||||  || ||||| ||||| || ||||| |||||||| || ||| | ||| | ||||| || ||||||||||| || ||||| ||||   | || ||    | || ||    || | ||| | |||  | |  | ||         |   || || |  || | ||     ||  | | ||  |                                                                                        
AAGCTGAGAAGGAGTTTAAGGTTGAAGTAGAAGCAATTGGACGAGTTCGACATAAAAATTTAGTGAGATTGCTTGGTTACTGTGCGGAAGGAGCTCATAGgtactttgttattgtctattgcttaatcctgcttgat-tgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtag

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ22711 (Selaginella moellendorffii), 5'ss of exon 3
AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtcatcccttcttcctgcccagtttgttgtgtggtggcgcagctccttgatgttctttgttgacctcgtttctggtggctgttgcag--
| || ||    || ||| ||||||||||||| ||||| ||| | ||  | ||||||||||| ||||| |||||||| ||||||| ||| ||     ||||||||    |||   |      | |  ||||| ||   |  |     ||||     |  | ||      |   |  ||  | | |||  |      
AGGCCGAACGAGAATTTCGAGTGGAAGTGGAGGCGATTGGAAGGGTGAGGCACAAGAATCTGGTGCGATTGCTGGGCTACTGTGTGGAAGGGAACTACAGgtgatatacat---tagacagtacaaagttttttccatctttcaaaagctagcctagctcctccaaacagtgctcttacgtttgcttctctttag

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: 34 (upstream exon), 32 (downstream exon)
Score: 11

AAGCGGAGAAGGAGTTTAGAGTGGAAGTGGAAGCGATCGGACGCGTTCGACACAAGAATCTCGTGCGCTTGCTGGGGTACTGTGCGGAGGGTGCTCACAGgtgaatgtca ... gctgttgcagGATGCTTGTGTACGAGTACGTGGATAATGGAAACTTGGAGCAGTGGCTGCATGGACCTCTGTCCCAAACAAATACACTTCCATGGGAAGCCCGCATGCGG




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