RetrogeneDB ID: retro_hsap_1122

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:56374211..56374817(-)
• Located in intron of: ENSG00000111540

Retrocopy information

• Ensembl ID: ENSG00000237493
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB13
• Ensembl ID: ENSG00000143545
• Aliases: None
• Description: RAB13, member RAS oncogene family [Source:HGNC Symbol;Acc:9762]

Sequence

>retro_hsap_1122
ATGGCCAAAGCCTACGACCACCTCTTCAAGTTGCTGCTGATCGGGGACTCGGGGGTGGGCAAGACTTGTCTGATCATTCG
CTTTGCAGAGGACAACTTCAACAACACTTACATCTCCACCATCGGAATTGATTTCAAGATCCGCACTGTGGATATAGAGG
GGAAGAAGATCAAACTACAAGTCTGGGACACAGCTGGCCAAGAGCGGTTCAAGACAATAACTACTGCCTACTACCGTGGA
GCCATGGGCATTATCCTAGCATACGACATCACGGATGAGAAATCTTTCGAGAATATTCAGAACTGGATGAAAAGCATCAT
GGAGAATGCCTCAGCTGGGGTGGAGCACCTCTTGCTAGGGAACAAATGTGACATGGAGGCCAAGAGGAAGGTGCAGAAGG
AGCAGGCCGATAAGTTGGCTCGAGAGCATGGAATCCGATTTTTCGAAACTAGTGCTAAATCCAGTATGAATGTGGATGAG
GCTTTTAGTTCCCTGGCCCGGGACATCTTGCTCAAGTCAGGAGGCCGGAGATCAGGAAACGGCAACAAGCCTCCCAGTAC
TGACCTGAAAACTTGTGACATAAAGAACACCAACAAGTGCTCCCTG

Alignment

ORF - retro_hsap_1122 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.02 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF
          MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF
Retrocopy MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF

Parental  KTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQADKLA
          KTITTAYYRGAMGIIL.YDITDEKSFENIQNWMKSI.ENASAGVE.LLLGNKCDMEAKRKVQKEQADKLA
Retrocopy KTITTAYYRGAMGIILAYDITDEKSFENIQNWMKSIMENASAGVEHLLLGNKCDMEAKRKVQKEQADKLA

Parental  REHGIRFFETSAKSSMNVDEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCDKKNTNKCSL
          REHGIRFFETSAKSSMNVDEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCD.KNTNKCSL
Retrocopy REHGIRFFETSAKSSMNVDEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCDIKNTNKCSL

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	0.14 RPM	176.62 RPM
bodymap2_adrenal	1.39 RPM	162.12 RPM
bodymap2_brain	0.14 RPM	34.36 RPM
bodymap2_breast	0.39 RPM	87.41 RPM
bodymap2_colon	0.10 RPM	193.61 RPM
bodymap2_heart	0.20 RPM	27.60 RPM
bodymap2_kidney	0.08 RPM	105.51 RPM
bodymap2_liver	0.13 RPM	42.71 RPM
bodymap2_lung	0.12 RPM	102.16 RPM
bodymap2_lymph_node	0.04 RPM	81.08 RPM
bodymap2_ovary	0.48 RPM	113.21 RPM
bodymap2_prostate	0.21 RPM	84.83 RPM
bodymap2_skeletal_muscle	0.09 RPM	28.10 RPM
bodymap2_testis	0.11 RPM	131.92 RPM
bodymap2_thyroid	0.26 RPM	90.31 RPM
bodymap2_white_blood_cells	0.00 RPM	4.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1122 was not detected

EST

No EST(s) were mapped for retro_hsap_1122 retrocopy.

TSS

No TSS is located nearby retro_hsap_1122 retrocopy 5' end.

Lab

retro_hsap_1122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1122 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_681

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017389	1 retrocopy	retro_cfam_1756,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Homo sapiens	ENSG00000143545	1 retrocopy	retro_hsap_1122 ,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Loxodonta africana	ENSLAFG00000032079	1 retrocopy	retro_lafr_45,
Macaca mulatta	ENSMMUG00000017586	1 retrocopy	retro_mmul_324,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.28 RPM
CEU_NA11930	0.72 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.21 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.38 RPM
FIN_HG00183	0.41 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.26 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.26 RPM
FIN_HG00375	0.42 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.34 RPM
GBR_HG00099	0.41 RPM
GBR_HG00111	0.19 RPM
GBR_HG00114	0.29 RPM
GBR_HG00119	0.36 RPM
GBR_HG00131	0.43 RPM
GBR_HG00133	0.27 RPM
GBR_HG00134	0.31 RPM
GBR_HG00137	0.44 RPM
GBR_HG00142	0.44 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.51 RPM
TSI_NA20513	0.75 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.48 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.33 RPM
TSI_NA20771	0.34 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.28 RPM
YRI_NA18916	0.29 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.21 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.31 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.27 RPM
YRI_NA19223	0.54 RPM

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Indel association:

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