RetrogeneDB ID: retro_hsap_4027

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:20791822..20792327(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000253866
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSG00000109084
• Aliases: TMEM97, MAC30
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_hsap_4027
TGCATGGAGTGGCTGCTGGGCCTCTACTTCCTCAGCCACAACCCCATCATCCTGTTCATGGACCTGTAGGCGGTGCTGCC
GTGCGAACTCTACCCAGTACAGTTTAGAAATCTGCTGAAGTGCTATGCTAAGGGGTTCAAAGGCCCGCTGCTACAGGAGC
CACCAGTTTGGTTTAAGTCCTTTCTGTTTTGCGAGCTTATGTTTCAGGTGCCTTTCTTTCCCATTGCAACCTATGCCTTC
CTCAAAGGAAGCTGCAACTGGATTCGAACCCCTGCAAATCATCTACTCAGTTCACACCATGATAACTTTAATTCCACTAC
TCTCCACATTTCTGTTGGAGGATTTCTCCAAAGCCAGTGGTTTCAAAGGATAAAGACCTGAGACTCTGCATGAACGGTTA
ACCCCTGTATCTGTCTATGCCCCCTACTTACTCATCCCATTCGTACTTTTAATTTTCATGTTGCAGAGCCCCTACTACAA
GTATGAGGAGAAAAGAAAAAAGAAA

Alignment

ORF - retro_hsap_4027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVEWLLGLYFLSHIPITLFMDLQAVLPRELYPVEFRNLLKWYAKEFKDPLLQEPPAWFKSFLFCELVFQL
          C.EWLLGLYFLSH.PI.LFMDL.AVLP.ELYPV.FRNLLK.YAK.FK.PLLQEPP.WFKSFLFCEL.FQ.
Retrocopy CMEWLLGLYFLSHNPIILFMDL*AVLPCELYPVQFRNLLKCYAKGFKGPLLQEPPVWFKSFLFCELMFQV

Parental  PFFPIATYAFLKGSCKWIRTPA-IIYSVHTMTTLIPILSTFLFEDFSKASGFKGQRPETLHERLTLVSVY
          PFFPIATYAFLKGSC.WIRTPA.IIYSVHTM.TLIP.LSTFL.EDFSKASGFKG.RPETLHERLT.VSVY
Retrocopy PFFPIATYAFLKGSCNWIRTPA>IIYSVHTMITLIPLLSTFLLEDFSKASGFKG*RPETLHERLTPVSVY

Parental  APYLLIPFILLIFMLRSPYYKYEEKRKKK
          APYLLIPF.LLIFML.SPYYKYEEKRKKK
Retrocopy APYLLIPFVLLIFMLQSPYYKYEEKRKKK

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	8.85 RPM
bodymap2_adrenal	0.00 RPM	8.39 RPM
bodymap2_brain	0.02 RPM	14.32 RPM
bodymap2_breast	0.00 RPM	8.48 RPM
bodymap2_colon	0.00 RPM	11.43 RPM
bodymap2_heart	0.00 RPM	3.12 RPM
bodymap2_kidney	0.00 RPM	10.40 RPM
bodymap2_liver	0.00 RPM	84.22 RPM
bodymap2_lung	0.00 RPM	19.48 RPM
bodymap2_lymph_node	0.00 RPM	5.41 RPM
bodymap2_ovary	0.00 RPM	44.99 RPM
bodymap2_prostate	0.00 RPM	55.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	15.91 RPM
bodymap2_testis	0.00 RPM	74.41 RPM
bodymap2_thyroid	0.00 RPM	12.65 RPM
bodymap2_white_blood_cells	0.00 RPM	3.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4027 was not detected

EST

No EST(s) were mapped for retro_hsap_4027 retrocopy.

TSS

No TSS is located nearby retro_hsap_4027 retrocopy 5' end.

Lab

retro_hsap_4027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4027 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2731
Gorilla gorilla	retro_ggor_2703
Pongo abelii	retro_pabe_3307
Macaca mulatta	retro_mmul_2323

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027 ,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,

Population studies

Expression level across human populations :

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

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Indel association:

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