RetrogeneDB ID: retro_hsap_2863

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:149699967..149701095(-)
• Located in intron of: ENSG00000070087

Retrocopy information

• Ensembl ID: ENSG00000224831
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSG00000163444
• Aliases: TMEM183A, C1orf37
• Description: transmembrane protein 183A [Source:HGNC Symbol;Acc:20173]

Sequence

>retro_hsap_2863
ATGGCCCGGGGGCCCGGCCCGCTAGGCAGGCCTCGCCCCGATACGGTCGCCATGCCCAAGAGAGGAAAGCGACTCAAGTT
CCGGGCCCACGACGCCTGCTCCGGCCGAGTGACCGTGGCGGATTACGCCGACTCGGATCTGGCGGTCGTGAGGTCTGGAC
GAGTCAAGAAAGCCGTAGCCAACGCTGTTCGGCAGGAAGTAAAATCTCTTTGTGGCTTGGAAGCCTCTCAGGTTCCTGCA
GAGGAAGCTCTTTCTGGGGCTGGTGAGCCCTATGACATCATCGACAGCAGTGATGAGATGGATGCCCAGGAGGAAAACAT
CCATGAGAGAACTGTCTCCAGAAAAAAGAAAAGCAAGAGACACAAAGAAGAACTGGACGGGGCTGGAGGAGAAGAGTATC
CCATGGATATTTGGCTATTGCTGGCCTCCTATATCCGTCCTGAGGACATTGTGAATTTTTCCCTGATTTGTAAGAATGCC
TGGACTGTCACTTGCACTGCTGCCTTTTGGACCAGGTTGTACCGAAGGCACTACACGCTGGATGCTTCCCTGCCTTTGCG
TCTGCGACCAGAGTCAATGGAGAAGCTGCACTGTCTCCGGGCTTGTGTGATCCGATCTCTGTACCATATGTATGAGCCAT
TTGCTGCTCGAATCTCCAAGAATCCAGCCATTCCAGAAAGCACCCCCAGCACATTAAAGAATTCCAAATGCTTACTTTTC
TGGTGCAGAAAGATTGTTGGGAACAGACAGGAACCAATGTGGGAATTCAACTTCAAGTTCAAAAAACAGTCCCCTAGGTT
AAAGAGCAAGTGTACAGGAGGATTGCAGCCTCCCGTTCAGTACGAAGATGTTCATACCAATCCAGACCAGGACTGCTGCC
TACTGCAGGTCACCACCCTCAATTTCATCTTTATTCCGATTGTCATGGGAATGATATTTACTCTGTTTACTATCAATGTG
AGCACGGACATGCGGCATCATCGAGTGAGACTGGTGTTCCAAGATTCCCCTGTCCATGGTGGTCGGAAACTGCGCAGTGA
ACAGGGTGTGCAAGTCATCCTGGACCCAGTGCACAGCGTTCGGCTCTTTGACTGGTGGCATCCTCAGTACCCATTCTCCC
TGAGAGCG

Alignment

ORF - retro_hsap_2863 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYANSDPAVVRSGRVKKAVANAVQQEVKSL
          MARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYA.SD.AVVRSGRVKKAVANAV.QEVKSL
Retrocopy MARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYADSDLAVVRSGRVKKAVANAVRQEVKSL

Parental  CGLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLL
          CGLEASQVPAEEALSGAGEP.DIIDSSDEMDAQEE.IHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLL
Retrocopy CGLEASQVPAEEALSGAGEPYDIIDSSDEMDAQEENIHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLL

Parental  LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLYHM
          LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKL.CLRACVIRSLYHM
Retrocopy LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLHCLRACVIRSLYHM

Parental  YEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ
          YEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ
Retrocopy YEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCTGGLQPPVQ

Parental  YEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRKLRSEQGV
          YEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRKLRSEQGV
Retrocopy YEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRKLRSEQGV

Parental  QVILDPVHSVRLFDWWHPQYPFSLRA
          QVILDPVHSVRLFDWWHPQYPFSLRA
Retrocopy QVILDPVHSVRLFDWWHPQYPFSLRA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.34 RPM	24.05 RPM
bodymap2_adrenal	0.18 RPM	36.11 RPM
bodymap2_brain	0.14 RPM	48.92 RPM
bodymap2_breast	0.25 RPM	28.04 RPM
bodymap2_colon	0.04 RPM	40.28 RPM
bodymap2_heart	0.20 RPM	11.34 RPM
bodymap2_kidney	0.12 RPM	34.41 RPM
bodymap2_liver	0.08 RPM	15.99 RPM
bodymap2_lung	0.46 RPM	30.98 RPM
bodymap2_lymph_node	0.04 RPM	39.11 RPM
bodymap2_ovary	0.50 RPM	33.54 RPM
bodymap2_prostate	0.19 RPM	42.12 RPM
bodymap2_skeletal_muscle	0.31 RPM	7.78 RPM
bodymap2_testis	0.53 RPM	42.34 RPM
bodymap2_thyroid	0.15 RPM	38.10 RPM
bodymap2_white_blood_cells	0.16 RPM	40.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2863 was not detected

EST

5 EST(s) were mapped to retro_hsap_2863 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA428099	149699994	149700426	99.8	431	1	430
AA722341	149699960	149700505	100	545	0	545
BF725692	149699959	149700454	100	495	0	495
BM794740	149700044	149700489	100	445	0	445
DA131547	149699843	149700470	100	627	0	627

TSS

No TSS is located nearby retro_hsap_2863 retrocopy 5' end.

Lab

retro_hsap_2863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2863 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863 , retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.28 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.25 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.17 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.21 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.17 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.19 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.27 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.18 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.12 RPM
YRI_NA19223	0.14 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).