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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT

Basic information

species Physcomitrella patens
transcript PP1S358_6V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 3'ss of exon 4
tttcttccctttcctttttacgtttgatttgttttgttttgttt-tgttttttttttttgttttttgt-tttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
  |   |   ||  ||  |    ||  ||   ||| | || |   ||||||||   | |||   |||   |   |  ||     ||    || | |    ||| | || || |||||||||||  | || || || || |||||||||||||||||||||||||| ||  |  | ||||   | |   |||| || || || 
--tgaactggtttgttgctgaactttgttcactttctcttctccctgttttttccatgtgtgaattgaactaaatcgaagaattatcactacctatctgcagGCTTGCTTACTTGCATGAGGCAATTGAACCCAAAGTGGTGCACCGTGATATCAAATCCAGCAATATATTGATTGATGATGATTTTGATGCCAAAGTATCA

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 3
-----------------------------tttcttccctttcctttttacgt----ttgatttgttttgttttgttttgttttttttttttgttttttg---ttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
                             |||||   | | | ||  | | |    || |||||     |||  || | ||||||||| |    || ||   | | | | || | ||     |||| || | | ||| |  |||||||||| ||||   ||||||||||||| |||||||| || ||||| || |||||||| ||  ||||   |  ||||||  | ||||| || 
gtgggtgaactatcatcaatgcttccgattttctcgtcatgcattgatgcatcttcttaatttgcagcttttgattgtttttttttttgtgaaattgtgtgatatatctcaattttgggggttgacatg-gttcagGATCACATATTTGCACGAGGGGCTGGAGCCGAAGGTGGTGCACCGGGACATCAAGTCGAGCAACATACTGCTGGACAAGAGATGGAACCCCAAGGTCTCG

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 3
-tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
  ||      |      ||||  |||| ||          |           |  |  ||   | |           |  | ||   |      |    |||||||| ||| | || ||||   |||| ||||||||||| |||||||| |||||| | |||||||||||| | ||   ||| ||||| ||||  || || 
gcttaaatgatcaagcctttatttttggttgaaaaaacaataaagatgcagatgatagtgaaatatccgaaaacctgacattcaacttc-tacatacccagGTTGGCTTATCTTCACGAGGGGCTGGAACCGAAGGTTGTTCACCGTGACATCAAAGCTAGCAACATTCTTCTTGACCAGCAGTGGAACGCTAGAGTATCC

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
             | |    | ||  || | || | | || |||  |   | | |||||   | |      |||   | |   |  |||  |   |  ||| | || ||||| ||||| ||  | || || || ||||||||||||||||||||||| ||||| || || || ||||   |||  ||||  ||| | |||
-------gtaagacatggaccattcaatattttgtctcttctttgatgcatatgttttgccatctaaggcatttt--tataattgatgatatactac-agGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G034855_T01 (Zea mays), 3'ss of exon 4
-tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
 |   |     | |  ||  |   |   |||  |   ||  |||||||  | | |   || |||    |      ||  ||   || | | ||||    ||| | || || |||||||||||  | || || || |||||||||||||| |||||||||||||| ||| |  | ||||   | |   |  | || || || 
ttaattgttgctacacttgcataatatgttttctcctttcagttttgtcatgtgtgaatgatttgaaatgaaaacaagagttttttat-atttgtccacagGCTTGCTTACTTGCATGAGGCGATTGAACCCAAAGTTGTGCACCGTGACATCAAATCCAGCAATATTTTGATTGATGATGAGTTCGAGTCCAAAGTATCA

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 3
---------------------------------------------tttcttccctttcct---ttttacgtt---tgatttgttttgtt--ttgttttgtttt---ttttttttgttttttgttttttttaaatgtgcattgtgacttgtgat-tagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
                                             || |||   |||      ||| | | |   |  | ||| |   |  |||||   ||||   |  | ||  |  |    | ||   || |     || |   || |||   || || || ||||||||||| | ||| ||||| || ||||||||||| ||||| |||||||| ||||||||| | |||    | |||||||| || || || 
gtgtgtttaatgttcattgagttttctttctccttttactgtgatttgcttatgtttatcgggtttcatgctctgtagtctgtatccatgattgttccattttatgtcatcttaatcatgctatcttgacaattaatttttctacattatgaaacagTTTAGCCTATTTGCATGAAGGTTTAGAGCCCAAAGTTGTGCACCGGGATATAAAATCCAGTAACATTCTTTTAGATAAAAACTGGAATGCCAAAGTATCA

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G22550.1 (Glycine max), 3'ss of exon 3
tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
    |    |    | | || | |   |     || | | ||  |  || ||    || | ||     |  ||| ||   ||| | | |||| |  ||||| | |||||||||||||| ||  | ||||| ||||| || ||||| |||||||| |||||||||||  |  | ||||   | |  ||||| ||||| |||
---gtgagttgctttgtctatgctccttcatgcttttgtagtcctcattcttagggttatcttagtgctaatttgaa---gcaatat-acttatt-ttagGCTTGCATATTTGCATGAAGCAATTGAGCCAAAGGTGGTACACCGAGATATCAAGTCCAGCAACATATTAATTGATGACGACTTTAATGCCAAGGTTTCT

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 3
tttcttccctttcctttttacgtttgatttgtt-ttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgat-tagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
|    |     | || | ||   |  ||   |  |||||    ||| | || | ||  || || |   | |    || |     || |   || |||   ||| | || ||| ||||||| | ||| || || || ||||||||||| ||||| |||||||| ||||||||| |||||    | |||||||| || || || 
taatgttatcatgctctgtagactgtatccatgattgttccagtttatgttatcttaatgattcta--tctcaacaattaatgtttctacattatgaaacagGCTAGCCTATCTGCATGAAGGTTTAGAACCCAAAGTTGTGCACCGGGATATAAAATCCAGTAACATTCTTTTGGATAAAAACTGGAATGCCAAAGTATCA

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ31013 (Selaginella moellendorffii), 3'ss of exon 3
tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
                       |   |||  || || | |             |    || |||  |||| ||   | | | ||| | ||| |    ||| || |||| |||||||| ||||||||||| ||||| || || || ||||||||| | ||||||||||||||||| | | | ||||| || ||| | |||
----------------------gtaagtttccttggtgtggacgaaagaaaccatcaaattcttttgttttctt---tttaccttgcgtcttctttacagGCTGACATACTTGCATGAAGCTTTGGAGCCCAAGGTGGTTCATCGGGATATCAAAGCAAGCAACATTCTTGTGGAGGGGGACTGGAACGCGAAGATATCT

upper sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ34699 (Selaginella moellendorffii), 3'ss of exon 3
tttcttccctttcctttttacgtttgatttgttttgttttgttttgttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
                       |   |||  || || | |             |     | |||  |||| ||   | | | ||| | ||| |    ||| || |||| |||||||| ||||||||||| ||||| || || || ||||||||| | ||||||||||||||||| | | | ||||| || ||| | |||
----------------------gtaagtttccttggtgtggacgaaagaaaccatcaaactcttttgttttctt---tttaccttgcgtcttctttacagGCTGACATACTTGCATGAAGCTTTGGAGCCCAAGGTGGTTCATCGGGATATCAAAGCAAGCAACATTCTTGTGGAGGGGGACTGGAACGCGAAGATATCT

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), 35 (downstream exon)
Score: 5

ATAATGGAAACTTGGAGCAGTGGCTGCATGGACCTCTGTCCCAAACAAATACACTTCCATGGGAAGCCCGCATGCGGATTGTCATGGGTACTGCTAAAGGgtgagtaagc ... ttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttttttttgttttttgttttttttaaatgtgcattgtgacttgtgattagGTTGGCATATTTGCATGAGGCTTTGGAGCCGAAGGTTGTGCACCGTGATATCAAATCCAGCAACATTCTTGTGGATGCGCAATGGAATGCTAAGGTGTCT
     ttttttttgttttttg  TA-rich tract