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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
--gtgaatccttttggtcatcctggtttgc---gttcataattatgtctgtttagttctggaaactctaatatgtttctgctttt---tcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
   ||||| ||||   |      ||| |||   ||    | ||     |      ||   |    ||  || |||||     | |   |||| || || || ||  | || ||||| |||||||||||| |||| ||||| || |||||||||||||||||||| |||||  | || ||||| ||||| |||
gtttgaattcttt--attcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAA-ATTATCATAGAC-----------------------
||   |  ||    || |||  |||| | |    |  |  ||     |||  |    |  |  |      |  |||| ||    |||||  |   | |  |     || | ||  ||||||||  ||| |     || |||     |  | | |  |  ||   |||||||| ||| | | |  |                       
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtag--ccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACC--AACCCAT----TTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 22
gtgaat-ccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|||  | || |||| || |    |||   | |     ||  || | | |  || |      ||   |   ||| || | |  ||| ||||| || ||| | ||||| ||||||||||| ||| | || |||||||||||||| ||||| ||||| || |||||  |||||||||||||||| || 
gtgtttgccctttgatcctaagtgttattgctttgcgtt-cgtgtttcttatttta-----tcctgtggctttttgatatg-cagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 22
gtga-atccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaac-tctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|||   |  |     | |||||    || ||| ||   | ||  |  ||  ||||       ||   | | ||| || | |  ||| |||||||| ||| | ||||| ||||||||||| ||  | || |||||||||||||| ||||| ||||| || |||||  |||||||||||||||| || 
gtggtgttttccctttgatccta---tgtgtt-attgctttgcattcttgtttcttattttatcctgtgtctttttgatatg-cagGAATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 22
gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaac-tctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|||  | |  || |  |||||    || ||| ||   | ||  |  ||  ||||       ||   | | ||| || | |  ||| |||||||| ||| | ||||| ||||||||||| ||  | || |||||||||||||| ||||| ||||| || |||||  |||||||||||||||| || 
gtgttttccctttg--atccta---tgtgtt-attgctttgcattcttgtttcttattttatcctgtgtctttttgatatg-cagGAATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 21
gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
     |  | |  ||  ||      | | ||  |  || ||      |   |    |  || |  ||  |||||   | | ||| ||||| || ||| | ||||| ||||| ||||| ||| | || |||||||||||||| ||||| ||||| || |||||  |||||||||| ||||| || 
----gtagtatctgttctctaatccttcattactttttgtgctcacatttctgattattctgtggtacttttcttggtatgcagGAATCGGCTTCGTTTGCTCACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
gt-gaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
|| | ||| |||   | |||||   || | ||     || ||   |  |  |||||   | ||     || | ||     | ||| ||||| || ||| | || || ||||| ||||| ||| | || |||||||||||||| ||||| ||||| || |||||  |||||||||| ||||| || 
gtagtatcttttctctaatcctacatttcttt-----ttgtgctcgcat--ttctgattattccg---tggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
---gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
    ||  ||| |    |   ||  ||| | |||||      | ||| |||| |||       | |  | ||  | || |||| |||||||||||||||| | ||||||||||||||||||||| | || |||||||||||||||||||||||||||||||||||  |||||||||| || ||||||
gtgatgtgtccctaccatatgccctgttcgggttcac-----tttctttttacttcaattgcttatgctttgcatgtggtttt-cagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAAATCATTATAGAC

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
----------------gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
                | |  |     ||   |  |   || | ||    | |||    |  | |  ||    |   || ||  |||   |  |||  || ||||| || || ||  | || || ||||| |||||||| || ||||| || ||||||||||||||||| || |||||  | || || || |||||||| 
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatagGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
                              ctctaat  putative branch site (score: 3)
                                      tgtttctgctttttc  CT-rich tract
                                 taatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG