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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG

Basic information

species Physcomitrella patens
transcript PP1S123_138V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 10
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                 |     |    ||    ||||| || |||| || |    |||   |  | ||   ||  | | |||  |             |||| ||| || |||||| ||     |||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| ||  | || |||||||| || |||||
-------------------------------------------------tgactgttttcttcacattattcatgtattcttatg--gcagtttgcataccacatgatacatttttctatgc---------tgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 6
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacaga-aggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                              |||| |||||  |  ||   | |  |   |  ||| | |  | |   | |  |  ||| |||   |  | | ||||| |    || |  |||   |||||||||||||||| ||||||||||| ||||| || || || || || |||||  | || |  || ||||| || ||
------------------------------------------------------------aattacgtattagctgtttaggtgcagatttatgggttttcaatttttgagagctgtttggatcttttgtagtaatatttgtagcttctc-ttcaatgcagTGTACTGGTTCATAGTGGTGGAGTTCATGGAGGACACTATTATGCCTTTATTCGTCCGAAGCTGTCTGATCAATG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 4
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                           | | |||   | | |   ||||| |  | ||  |  |  |||     |     | |           |  | | ||| ||  | |  | | ||  |  |||||| || ||||| |||||||| |||||||||||||| ||||| || || ||  | || ||  | ||||| || ||
---------------------------------------------------------tatatctacagttcagtccttttttcttctccaccacctaagcca-acacttgcttctgcaattctttgtgtactaatactgtttatcatcttttatt--cagTGTTCTTGTTCATAGTGGTGGGGTACATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 2
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                       || |||| | | |  ||||  |    || ||  |  |   | ||  || |||  |  |    |     |      || | ||   ||||    | ||  |  ||||||  ||||||||||||| || || |||||||| ||||| || ||||||||||| || || |||||||| |||||
------------------------------------------------------ttctctttatccattctaatgaaggaattgctatccaa---tttgttttatgcatatttaatctatgaagttctgcttaacat--actttaaaatttttctc-cagTGTTTTGGTTCACAGTGGAGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCAACCCTCTCTGAACAGTG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 10
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                            || |    |  ||  ||  |    | | |||| ||||| | |    ||| |  |   ||   |    || |     ||    |  |  ||| |    |||||           ||| ||  |||||||||||||||| || |||||||| ||||| || ||||||||||| || || || ||||| |||||
--------------------------------------------tgctgatgatgtctattagtgtgcaattatttctttttatgt----gaatgcatatttttatctgcgatgttcattat----ttgacagatttaaattttttcc--------acagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 10
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                             | |    |  ||| ||  |    | | |||| ||||| | |    ||| |  |   ||        || | |    | || | | ||||    |  | |||||| | |    ||| ||  |||||||||||||||| || |||||||| ||||| || ||||||||||| || || || ||||| |||||
-------------------------------------------gggctgatgatgtccattagtgtgcaattatttgtttttatgt----gaatgcatattttt-------atctgtgatgt-gcattatttgac--cgattattttttttcca---cagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCAACTCTATCTGAGCAGTG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 10
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtg-gcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                              |   ||  |   |  |    ||  | |     ||   |    ||  ||||| ||||     |    ||||  ||||   | |   ||||| ||  |||||||  |||||||||||||||| || |||||||| ||||| || |||| ||| || || ||||||||||| |||||
-----------------------------------------------------------cactagtttgatggat-gtcccattaatgctatcagtaaacagattgttaaaatgtattattatggtagaattcctatta-ttctcaattgtttgtctgcagTGTTTTGGTTCACAGTGGTGGGGTGCATGGTGGACATTATTATGCTTATATAAGGCCAACACTCTCTGATCAGTG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 10
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                                                 |  |||| |     || | ||  ||  | |||||       || | | |   |||   ||||||  ||   || |  | |  |  ||    | ||||   |||  | | ||||| || ||||||||||| ||||| |||||||| ||||| || || ||||| |||||||| || ||||| |||||
-----------------------------------------------actgaacattcgggaatagt-atatatcaagttttt-------gatgcttta--ttgatgcaaaatggatactattgttt-atctcttac--acattttgacgttgtttgtagTGTTCTAGTTCACAGTGGCGGAGTGCATGGTGGACATTATTATGCCTTTATAAGACCCACCCTTTCTGATCAGTG

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: 7

GCTATGAGTTTCCACTGCAACTAGACTTGGATAGGGAGAACGGAAAGTACCTCTCTCCTGATGCCGACCGTAGTGTTCGAAATTTGTACACCTTGCACAGgtttggggca ... ttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
                       aattgat  putative branch site (score: 7)
                                   cttttttttgttcgt  putative PPT
                                    ttttttttgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG