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Table 1 The palindromic duplication of the gene pair between ATP-regulated IRK and G-protein-activated IRK genes on a chromosome.

From: Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

Properties

Pair

Homolog

Summary of Expression

Hox-location

Chromosome

Chrom-location and direction

Distance between the pair in bp

Genes in branches with green color figures in Fig. 5

palindromic

GG-Kcnj1/AR

Kir1.1/ROM-K/ATP-regulated

  

GG-chromosome-24

1.06 Mb-reverse

31795

 

GG-Kcnj5/G

GIRK4/Kir3.4/KATP-1

 

PKNOX2-24-0.14bM

GG-chromosome-24

1.09 Mb-forward

 

palindromic

HS-Kcnj1/AR

Kir1.1/ROM-K/ATP-regulated

Kcnj1-Kidney epithelium

 

HS-chromosome-11

128.2 Mb-reverse

24045

 

HS-Kcnj5/G

GIRK4/Kir3.4/KATP-1

Kcnj5-Heart muscle cell

 

HS-chromosome-11

128.3 Mb-forward

 

palindromic

MM-Kcnj1.1/AR

Kir1.1/ROM-K/ATP-regulated

  

MM-chromosome-9

32.4 Mb-forward

80347

 

MM-Kcnj5/G

GIRK4/Kir3.4/KATP-1

  

MM-chromosome-9

32.3 Mb-reverse

 

palindromic

RN-Kcnj1/AR

Kir1.1/ROM-K/ATP-regulated

  

RN-chromosome-8

32.2 Mb-forward

22000

 

RN-Kcnj5/G

GIRK4/Kir3.4/KATP-1

an annotated genomic sequence(NW_047799) using the gene prediction method: GNOMON*1

 

RN-chromosome-8

32.1Mb-reverse

 

Genes in branches with orange color figures in Fig. 5

palindromic

HS-Kcnj10/AR

Kir4.1/Kir1.2/ATP-regulated

Kcnj10-glia

 

HS-chromosome-1

157.2 Mb-reverse

11322

 

HS-Kcnj9/G

GIRK3/Kir3.3

Kcnj9-neuronal cell

 

HS-chromosome-1

157.3 Mb-forward

 

palindromic

MM-Kcnj10/AR

Kir4.1/ATP-regulated

  

MM-chromosome-1

172.4 Mb-forward

12138

 

MM-Kcnj9/G

GIRK3/Kir3.3

  

MM-chromosome-1

172.4 Mb-reverse

 

palindromic

RN-Kcnj10/AR

KIR4.1/Kir1.2/ATP-regulated

  

RN-chromosome-13

88.5 Mb-forward

24712

 

RN-Kcnj9/G

GIRK3/Kir3.3/Kir3.1

  

RN-chromosome-13

88.5 Mb-reverse

 

Genes in branches with blue color figures in Fig. 5

palindromic

GG-Kcnj15/AR

Kir4.2/Kir1.3

 

HOXC8-1-87Mb(stand alone)

GG-chromosome-1

101.25 Mb-forward

275125

 

GG-Kcnj6/G

GIRK2/Kir3.2/KATP-2

 

HOXC8-1-87Mb

GG-chromosome-1

100.9 Mb-reverse

 

palindromic

HS-Kcnj15/AR

Kir4.2/Kir1.3

Kcnj15-kidney, epithelium, glia

 

HS-chromosome-21

38.5 Mb-forward

339968

 

HS-Kcnj6/G

GIRK2/Kir3.2/KATP-2

Kcnj6-Neuronal cell

 

HS-chromosome-21

37.9 Mb-reverse

 

palindromic

MM-Kcnj15/AR

Kir4.2/Kir1.3

  

MM-chromosome-16

95.9803Mb-forward

260226

 

MM-Kcnj6/G

GIRK2/Kir3.2/KATP-2

  

MM-chromosome-16

95.5 Mb-reverse

 

palindromic

RN-Kcnj15/AR

Kir4.2/Kir1.3

  

RN-chromosome-11

35.6 Mb-forward

460583

 

RN-Kcnj6/G

GIRK2/Kir3.2/KATP-2

  

RN-chromosome-11

35.1 Mb-reverse

 

Genes in branches with purple color figures in Fig. 5

disperse

GG-Kcnj3/G

GIRK1/KIR3.1

 

HOXD(13)-7-17.1Mb-r

GG-chromosome-7

36.4 Mb-forward

 

Palindromic?

HS-Kcnj13/AR

Kir7.1/ATP-related

Kcnj13-choroid plexus/thyroid/intestine

HOXD-2q31.1-176.8Mb-f

HS-chromosome-2

233.8 Mb-reverse

78000000

 

HS-kcnj3/G

GIRK1/Kir3.1

Kcnj3-neuronal cell (heteromer with Kcnj6, 9)

HOXD-2q31.1-176.8Mb-f

HS-chromosome-2

155.8 Mb-forward

possibly paired with Kcnj13

   

Kcnj3-heart muscle cell (heteromer with Kcnj5)

    

disperse

MM-Kcnj3/G

GIRK1/Kir3.1

 

HOXD-2-45.0 cM-74.56Mb-f

MM-chromosome-2

55.4 Mb-forward

 

disperse

RN-Kcnj3/G

GIRK1/KIR3.1

 

HOXD-3-57.3Mb-f

RN-chromosome-3

37.0 Mb-forward

 

Genes in branches with red color figures in Fig. 5

tandem

GG-Kcnj16

Kir5.1

  

GG-chromosome-18

7.95 Mb-Forward

14689

 

GG-Kcnj2

Kir2.1

  

GG-chromosome-18

7.97 Mb-Forward

 

tandem

HS-Kcnj16

Kir5.1

colocalize with Kcnj2 in brain and in kidney

HOXB-17q21-q22-44.06Mb-r

HS-chromosome-17

68.7 Mb-Forward

33932

 

HS-Kcnj2

Kir2.1

Heart (Andersen Syndrome), Vas. Smooth muscle

HOXB-17q21-q22-44.06Mb-r

HS-chromosome-17

68.8 Mb-Forward

 

tandem

MM-Kcnj16

Kir5.1

 

HOXB-11-56.08cM-95.87Mb-f

MM-chromosome-11

110.7 Mb-Forward

39324

 

MM-Kcnj2

Kir2.1

 

HOXB-11-56.08cM-95.87Mb-f

MM-chromosome-11

110.7 Mb-Forward

 

tandem

RN-Kcnj16

KIR5.1

 

HOXB-10-84.95Mb-f

RN-chromosome-10

100.5 Mb-Forward

59504

 

RN-Kcnj2

Kir2.1/Kir2.2

 

HOXB-10-84.95Mb-f

RN-chromosome-10

100.6 Mb-Forward

 
 

DR-Kcnj2.1

Kir1.1/Kir3.1

 

Zebra-HOXB

DR-chromosome-3

2.0 Mb

 
  1. *1 Noted in NCBI genome project Rat. Predicted protein amino acid sequence was devoid of the major part of C-terminal distal to the feature sequence of Kcnjs. Therefore the AA sequence was not included in the construction of the phylogenetic tree in Fig. 5.
  2. From the survey of the established genome databases, all gene pairs within IRK genes as far as thoroughly looked for are illustrated. In addition, the lower four pairs illustrate the tandem duplications of IRK genes in the elementary IRK group. Some of these tandem duplications in the human genome were reported previously [33]. Respective groups of genes which corresponded to the character colors in Fig. 8 are indicated.
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BMC Ecology and Evolution

ISSN: 2730-7182

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