RNA ligase 1

The RLIG1 gene is located on the positive strand at 12q21.32 in humans (p = short arm, q = long arm). It has 7 exons and 6 introns. The gene spans from 88,035,536 to 88,050,160 with 14,645 base pairs. There is only one isoform of the transcript, which is the transcript of this gene itself.^[5]

Neighbor genes around human RLIG1 are: C12orf50 (-), RNA5SP364 (+), LOC107984542 (-), LOC100420011 (+), CEP290 (-).

The RLIG1 gene is ubiquitously expressed in 27 tissues.^[5] It is expressed a little bit higher in esophagus, skin, brain and bone marrow.^[5] It showed increased expression in several tumor cells and tissues such as in colorectal tumor tissue,^[7] in ovarian cancer epithelial cells,^[8] and in hyperplastic enlarged lobular units epithelial cells.^[9]

RLIG1 protein has 325 amino acids.^[10] The molecular weight is 37.5 kD, and the isoelectric point is 6.6 pH.^[11] It is not a membrane protein, and it stays in the cytosol.^[12] For the content of the amino acids, compared with other human proteins, RLIG1 is high in asparagine and histidine, but it is low in alanine.^[11] There are no validated domains or motifs.^[10] It has a short repetitive structures of "INGNP", but it is not conserved in orthologs.^[11] However, there are two highly conserved predicted motifs. They are the protease caspase 3 and 7 cleavage motif, and the mitogen-activated protein kinase (MAPK) docking motif.^[13][14] There are several predicted protein kinase c phosphorylation sites and casein kinase II phosphorylation sites, but they are not conserved in orthologs.^[13][14]

         1  MKRLGSVQRK MPCVFVTEVK EEPSSKREHQ PFKVLATETV SHKALDADIY SAIPTEKVDG
        61  TCCYVTTYKD QPYLWARLDR KPNKQAEKRF KNFLHSKENP KEFFWNVEED FKPAPECWIP
       121  AKETEQINGN PVPDENGHIP GWVPVEKNNK QYCWHSSVVN YEFEIALVLK HHPDDSGLLE
       181  ISAVPLSDLL EQTLELIGTN INGNPYGLGS KKHPLHLLIP HGAFQIRNLP SLKHNDLVSW
       241  FEDCKEGKIE GIVWHCSDGC LIKVHRHHLG LCWPIPDTYM NSRPVIINMN LNKCDSAFDI
       301  KCLFNHFLKI DNQKFVRLKD IIFDV

NCL and LRRK2 was experimentally determined to interacted with RLIG1.^[19] NCL physically interacted with RLIG1, and LRRK2 was associated with RLIG1.^[19] There are several predicted protein interactions for RLIG1. The interactions with PNN, OTUD68, and ACTR6 were predicted by co-expression.^[20]

Orthologs of RLIG1 protein are found within the mammals, birds, reptiles, amphibians, fishes, and invertebrates.^[21] The length and contents of the protein sequence was highly conserved in the selected orthologs (table below).^[18] It is important to notice that the RLIG1 protein was only found in mollusks, tunicate, and cephalochordata in invertebrates, but it was not found in insects, arachnids, crustaceans, corals, worms, jellyfishes, sponges within the other groups in invertebrates.^[17][22] RLIG1 protein was not found in bacteria, fungi, and viruses.^[17] There is no paralog for RLIG1 protein.^[17] The mutation rate of RLIG1 was close to that of fibrinogen alpha chain. The human's RLIG1 protein was more closely related to the sheep's ortholog than to the mouse's ortholog. The invertebrates RLIG1 orthologs were mostly distantly related to the human protein.

Ortholog table

Selected Orthologs Table of RLIG1 Protein^{[18][21][17][22][23]}

Sequence Number	Ortholog Group	Genius and Species	Taxonomic Group	Common Name	Time Since Divergence (Estimated MYA)	Accession Number	Sequence Length (aa)	Sequence Identity	Sequence Similarity
1	Mammals	Homo sapiens	Primates	Human	0	NP_001009894.2	325	100%	100%
2	Mammals	Mus musculus	Rodentia	House Mouse	90	NP_780337.2	327	84%	90%
3	Mammals	Ovis aries	Artiodactyla	Sheep	96	NP_001186723.1	325	91%	96%
4	Mammals	Phascolarctos cinereus	Diprotodontia	Koala	159	XP_020849155.1	325	86%	92%
5	Mammals	Ornithorhynchus anatinus	Monotremata	Platypus	177	XP_028934667.1	326	78%	89%
6	Aves	Gallus gallus	Galliformes	Chicken	312	XP_040518235.1	324	75%	86%
7	Aves	Cygnus atratus	Anseriformes	Black Swan	312	XP_035407728.1	324	75%	86%
8	Aves	Calypte anna	Apodiformes	Anna's Hummingbird	312	XP_030312194.1	324	75%	87%
9	Reptiles	Crocodylus porosus	Crocodylia	Australian Saltwater Crocodile	312	XP_019400824.1	323	76%	88%
10	Reptiles	Zootoca vivipara	Squamata	Common Lizard	312	XP_034983157.1	325	71%	85%
11	Reptiles	Python bivittatus	Squamata	Burmese Python	312	XP_007429130.1	323	70%	84%
12	Reptiles	Dermochelys coriacea	Testudines	Leatherback Sea Turtle	312	XP_038257651.1	325	78%	90%
13	Amphibians	Bufo bufo	Anura	Common Toad	351.8	XP_040264560.1	324	63%	77%
14	Amphibians	Rhinatrema bivittatum	Gymnophiona	Two-lined Caecilian	351.8	XP_029457527.1	335	66%	82%
15	Fishes	Danio rerio	Cypriniformes	Zebrafish	435	NP_001008606.1	325	60%	79%
16	Fishes	Rhincodon typus	Orectolobiformes	Whale Shark	473	XP_020369226.1	330	56%	73%
17	Invertebrates	Styela clava	Stolidobranchia	Asian Tunicate	676	XP_039256956.1	351	44%	59%
18	Invertebrates	Branchiostoma floridae	Amphioxiformes	Florida Lancelet	684	XP_035678444.1	341	43%	62%
19	Invertebrates	Pecten maximus	Pectinida	King Scallop	797	XP_033752428.1	347	44%	62%
20	Invertebrates	Crassostrea gigas	Ostreida	Pacific Oyster	797	XP_034327602.1	357	41%	59%