RetrogeneDB ID: retro_hsap_171

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:77165440..77166220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226415
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSG00000268548
• Aliases: None
• Description: triosephosphate isomerase 1 [Source:HGNC Symbol;Acc:12009]

Sequence

>retro_hsap_171
GACACTGACCTTCAGCGCCTCGGCTCCAGCGCCATGGCGCCCTCCAGGAAGTTCTTCGTTGGGGGGAACTGGAAGATGAA
CGGGCGAAAGCAGAGTCTGCGGGAGCTCGTCCGCACTCTGAACGCGGCCAAGGTGCCGGCCGACACCGAGGTGGTTTGTA
CTCCGCCTACTGCCTATATCGACTTCGCCCGGCAGAAGCTAGATCCCAAGATTGCTGTGGCTGCGCAGAACTGCTACAAA
GTGACTAATGGGGCTTTTACTGGGGAGATCAGCCCTGGCATGATCAAAGACTGCAGAGCCACGTGGGTGGTCCTGGGGCA
CTCAGAGAGAAGGCATGTCTTTGGGGAGTCAGATGAGCTGATTGGGCAGAAAGTGGCCCATGCTCTGGCAGAGGGACTCG
GAGTAATCGCCTGCACTGGGGAGAAGCTAGATGAAAGGGAAGCTGGCATCACTGAGAAGGTTGTTTTCGAGCAGACAAAG
GTCATCGCAGATAACGTGAAGGACTGGAGCAAGGTCGTCCTGGCCTATGAGCCTGTGTGGGCCATTGGTACTGGCAAGAC
TGCAACACCCCAACAGGACCAGGAAGTACACGACAAGCTCCGAGGATGGCTTAAGTCCAACGTCTCTGATGCGGTGGCTC
AGAGCACCCGTATCATTTATGGAGGCTCTGTGACTGGGGCAACCTGCAAGGAGCTGGCCAGCCAGCCTGGCGTGGATGGC
TTCCTTGTGGGTGGTGCTTCCCTCAAGCCCGAATTCGTGGACATCATCAATGCCAAACAA

Alignment

ORF - retro_hsap_171 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.54 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DTDLQRLGSSAMAPSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPK
          DTDLQRLGSSAMAPSRKFFVGGNWKMNGRKQSL.EL..TLNAAKVPADTEVVC.PPTAYIDFARQKLDPK
Retrocopy DTDLQRLGSSAMAPSRKFFVGGNWKMNGRKQSLRELVRTLNAAKVPADTEVVCTPPTAYIDFARQKLDPK

Parental  IAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACIG
          IAVAAQNCYKVTNGAFTGEISPGMIKDC.ATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIAC.G
Retrocopy IAVAAQNCYKVTNGAFTGEISPGMIKDCRATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACTG

Parental  EKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSD
          EKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQ.QEVH.KLRGWLKSNVSD
Retrocopy EKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQDQEVHDKLRGWLKSNVSD

Parental  AVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          AVAQSTRIIYGGSVTGATCKELASQP.VDGFLVGGASLKPEFVDIINAKQ
Retrocopy AVAQSTRIIYGGSVTGATCKELASQPGVDGFLVGGASLKPEFVDIINAKQ

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	0.04 RPM	0.00 RPM
bodymap2_adrenal	0.35 RPM	0.00 RPM
bodymap2_brain	0.49 RPM	0.00 RPM
bodymap2_breast	0.12 RPM	0.00 RPM
bodymap2_colon	0.25 RPM	0.00 RPM
bodymap2_heart	0.17 RPM	0.00 RPM
bodymap2_kidney	0.70 RPM	0.00 RPM
bodymap2_liver	0.06 RPM	0.00 RPM
bodymap2_lung	0.09 RPM	0.00 RPM
bodymap2_lymph_node	0.18 RPM	0.00 RPM
bodymap2_ovary	0.15 RPM	0.00 RPM
bodymap2_prostate	0.10 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.29 RPM	0.00 RPM
bodymap2_testis	0.30 RPM	0.00 RPM
bodymap2_thyroid	0.45 RPM	0.00 RPM
bodymap2_white_blood_cells	0.16 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_171 was not detected

EST

No EST(s) were mapped for retro_hsap_171 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_96744	101 libraries	185 libraries	1048 libraries	363 libraries	132 libraries

The graphical summary, for retro_hsap_171 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_171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_171 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_160
Gorilla gorilla	retro_ggor_151

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000268548	1 retrocopy	retro_hsap_171 ,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.87 RPM
CEU_NA11843	1.54 RPM
CEU_NA11930	4.40 RPM
CEU_NA12004	1.22 RPM
CEU_NA12400	1.82 RPM
CEU_NA12751	1.36 RPM
CEU_NA12760	4.90 RPM
CEU_NA12827	2.50 RPM
CEU_NA12872	1.93 RPM
CEU_NA12873	1.63 RPM
FIN_HG00183	2.28 RPM
FIN_HG00277	1.89 RPM
FIN_HG00315	1.85 RPM
FIN_HG00321	2.48 RPM
FIN_HG00328	1.66 RPM
FIN_HG00338	1.96 RPM
FIN_HG00349	2.76 RPM
FIN_HG00375	1.98 RPM
FIN_HG00377	1.61 RPM
FIN_HG00378	1.27 RPM
GBR_HG00099	2.47 RPM
GBR_HG00111	0.95 RPM
GBR_HG00114	1.47 RPM
GBR_HG00119	1.29 RPM
GBR_HG00131	1.35 RPM
GBR_HG00133	1.54 RPM
GBR_HG00134	1.42 RPM
GBR_HG00137	1.40 RPM
GBR_HG00142	1.00 RPM
GBR_HG00143	1.34 RPM
TSI_NA20512	1.55 RPM
TSI_NA20513	1.35 RPM
TSI_NA20518	4.16 RPM
TSI_NA20532	1.16 RPM
TSI_NA20538	1.52 RPM
TSI_NA20756	3.81 RPM
TSI_NA20765	1.08 RPM
TSI_NA20771	1.93 RPM
TSI_NA20786	1.41 RPM
TSI_NA20798	1.53 RPM
YRI_NA18870	3.01 RPM
YRI_NA18907	1.98 RPM
YRI_NA18916	1.58 RPM
YRI_NA19093	1.67 RPM
YRI_NA19099	2.40 RPM
YRI_NA19114	2.07 RPM
YRI_NA19118	1.12 RPM
YRI_NA19213	1.55 RPM
YRI_NA19214	1.11 RPM
YRI_NA19223	0.82 RPM

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Indel association:

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