RetrogeneDB ID: retro_hsap_4252

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:37636687..37637290(-)
• Located in intron of: ENSG00000255872

Retrocopy information

• Ensembl ID: ENSG00000233111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSG00000174903
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_hsap_4252
ATGAACCCCGGATATGACTGCCTGTTTAAGCTGCTTTTGATTGGCGACTCAGGCGTGGGCAAGTCATGCCTGCTCCTGCG
GTTTGCTGATGACCCTTACACAGAGAGCTACATCAGCACCATCGGGGTGGACTTCAAGATCCAAACCATCGAGCTGGATG
GCAAAACTATCAAACTTCAGATCTGGGACACGGCGGGCCAGGAACGGTTCTGGACCATCACTTCCAGCTACTACCGGGGG
GCTCATGGCTTCCTCGTGGTATATGACGTCACTGACCAGGAATCCTATGCCAACGTGAAGCAGTGGCTGCAGGAGATTGA
CCGCCATGCCAGCGAGAACGTCAATAAGCTCCTGGTGGGCAACAAGAGCGACCTCACCACCAAGAAGGTGGTGGACAACA
CCACAGCCAAGGAGTTTGCAGACTCTTTGGGCATCCCCTTCTTGGAGACGAGTGCCAAGAATGCCACCAATGTCGAGCAG
GCGTTCATGACCATGGCTGCTGAGATCAAAAAGCAGATGGGGCCCGGAGCAGCCTCCGGGGGCGAGCGGCCCAATCTCAA
GATCGACAGCACCCCTGTAAAGCCGGCTGGCGGTGGTTGTTGC

Alignment

ORF - retro_hsap_4252 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
          MNP.YD.LFKLLLIGDSGVGKSCLLLRFADD.YTESYISTIGVDFKI.TIELDGKTIKLQIWDTAGQERF
Retrocopy MNPGYDCLFKLLLIGDSGVGKSCLLLRFADDPYTESYISTIGVDFKIQTIELDGKTIKLQIWDTAGQERF

Parental  RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFA
          .TITSSYYRGAHG..VVYDVTDQESYANVKQWLQEIDR.ASENVNKLLVGNKSDLTTKKVVDNTTAKEFA
Retrocopy WTITSSYYRGAHGFLVVYDVTDQESYANVKQWLQEIDRHASENVNKLLVGNKSDLTTKKVVDNTTAKEFA

Parental  DSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC
          DSLGIPFLETSAKNATNVEQAFMTMAAEIKK.MGPGAASGGERPNLKIDSTPVKPAGGGCC
Retrocopy DSLGIPFLETSAKNATNVEQAFMTMAAEIKKQMGPGAASGGERPNLKIDSTPVKPAGGGCC

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	0.00 RPM	110.48 RPM
bodymap2_adrenal	0.06 RPM	75.29 RPM
bodymap2_brain	0.00 RPM	39.26 RPM
bodymap2_breast	0.00 RPM	83.79 RPM
bodymap2_colon	0.00 RPM	73.34 RPM
bodymap2_heart	0.00 RPM	34.43 RPM
bodymap2_kidney	0.02 RPM	52.71 RPM
bodymap2_liver	0.00 RPM	31.26 RPM
bodymap2_lung	0.00 RPM	61.39 RPM
bodymap2_lymph_node	0.02 RPM	56.08 RPM
bodymap2_ovary	0.02 RPM	84.61 RPM
bodymap2_prostate	0.00 RPM	66.44 RPM
bodymap2_skeletal_muscle	0.04 RPM	55.87 RPM
bodymap2_testis	0.06 RPM	74.87 RPM
bodymap2_thyroid	0.02 RPM	87.72 RPM
bodymap2_white_blood_cells	0.02 RPM	81.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4252 was not detected

EST

No EST(s) were mapped for retro_hsap_4252 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_193261	603 libraries	837 libraries	383 libraries	6 libraries	0 libraries
TSS #2	TSS_193262	1310 libraries	472 libraries	38 libraries	5 libraries	4 libraries

The graphical summary, for retro_hsap_4252 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4252 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2892
Gorilla gorilla	retro_ggor_2850
Pongo abelii	retro_pabe_3386

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931,
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 ,
Gorilla gorilla	ENSGGOG00000009755	2 retrocopies	retro_ggor_1792, retro_ggor_2850,
Macropus eugenii	ENSMEUG00000000023	1 retrocopy	retro_meug_1985,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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