RetrogeneDB ID: retro_hsap_1652

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:74701640..74702442(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000262904
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMPO
• Ensembl ID: ENSG00000120802
• Aliases: TMPO, CMD1T, LAP2, LEMD4, PRO0868, TP
• Description: thymopoietin [Source:HGNC Symbol;Acc:11875]

Sequence

>retro_hsap_1652
ACAACCAGGAAGCTGTATGAGAAATAGCTTTTGAAACTGAGGGAGCAAGGAACAGAATCAAGATCGTCTCCTTCAGCAAC
AATTTCTTCTTCAGCAGAAAATACAAGGCAGAATGGAAGTAATGATTCTGACAGATATGGTGAAAATGAAGAAGACTCTA
AATTGGGCTCAAGTTTGAGAAGAGAGAACCGCTAAACAGGGGAGTAAAGACTCCAGTAACCCTCAAGCAAAGAAGAGTTG
AGCACAAGGAGAGCTATTCTCAAGCTGGAATAACTGGGACTGAATGGACAAGTGGATCTTCAAAAGGCGGACCTCTGCAG
GCATTATTAACTAGGGAATCTACAAGAGGGTCAAGAAGAACTCCAAGCAAAAGGGTGCACGCTTCAGAATATTTTCGTAT
AGATGGAGCAGTAATTTCAGCGAGTACTCCCATAGCTGAAACTATAATTGCTTCAAACAACGAATCCTTAATTGTCAATA
GGGTGACTGGAAATTTCAAGCATGCATTTCCTATTCTGCCAGTCACTGAATTCTCAGACATACCCAGAAGAACACCAAAG
AAACCATTGACAAGAGCTGAAGTGGGAGAAAAAAAACACAGGAAAGAAGAGTAGAAAGGGATATTCTTAAGGAAATGTTC
CCCTATGAAGCAACTACACCAACAAGAATTAGTGCTAGTTGCCGCAGAACAATCAAAGGAGCTGCAGGCCGGCCATTAGA
ACTCAGTGATTTGAGGATGGAGGAGTCGTTTTCATCTACATATGTTCCTAAGTATGTTCCCTTGGCAGACGTCAAGTGAG
AA

Alignment

ORF - retro_hsap_1652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 58.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSK-IELKLEKREPLKGR
          TTRKLYEK.LLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRY..NEEDSK.I.LK.EKREPL...
Retrocopy TTRKLYEK*LLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYGENEEDSK<IGLKFEKREPLNRG

Parental  AKTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVETSEHFRIDGPV
          .KTPVTLKQRRVEH..SYSQAGIT.TEWTSGSSKGGPLQA.LTRESTRGSRRTP.KRV..SE.FRIDG.V
Retrocopy VKTPVTLKQRRVEHKESYSQAGITGTEWTSGSSKGGPLQALLTRESTRGSRRTPSKRVHASEYFRIDGAV

Parental  ISESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGEKTEERRVERDI
          IS.STPIAETI.AS.NESL.VNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVG...........I
Retrocopy ISASTPIAETIIASNNESLIVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGXXXHRKEE*KGI

Parental  -LKEMFP-YEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPLADVKSE
          .L....P.YEA.TPT.ISASCRR.IKGAAGRPLELSD.RMEESFSS.YVPKYVPLADVK.E
Retrocopy FLRKCSP<YEATTPTRISASCRRTIKGAAGRPLELSDLRMEESFSSTYVPKYVPLADVK*E

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	38.36 RPM
bodymap2_adrenal	0.00 RPM	96.82 RPM
bodymap2_brain	0.00 RPM	41.47 RPM
bodymap2_breast	0.00 RPM	35.62 RPM
bodymap2_colon	0.00 RPM	68.93 RPM
bodymap2_heart	0.00 RPM	24.29 RPM
bodymap2_kidney	0.00 RPM	84.94 RPM
bodymap2_liver	0.00 RPM	45.77 RPM
bodymap2_lung	0.00 RPM	83.18 RPM
bodymap2_lymph_node	0.15 RPM	148.09 RPM
bodymap2_ovary	0.00 RPM	150.44 RPM
bodymap2_prostate	0.00 RPM	78.91 RPM
bodymap2_skeletal_muscle	0.00 RPM	29.26 RPM
bodymap2_testis	4.94 RPM	99.19 RPM
bodymap2_thyroid	0.00 RPM	58.58 RPM
bodymap2_white_blood_cells	0.00 RPM	208.47 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1652 in 52 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001VKU	POLR2A	16:74700533..74701014
ENCFF002CFW	POLR2A	16:74700533..74700902
ENCFF002CFX	POLR2A	16:74700551..74700906
ENCFF002CGN	POLR2A	16:74700617..74700862
ENCFF002CHO	POLR2A	16:74700227..74700960
ENCFF002CIH	POLR2A	16:74700547..74700877
ENCFF002CIO	POLR2A	16:74700519..74700901
ENCFF002CJE	POLR2A	16:74700476..74700979
ENCFF002CJZ	POLR2A	16:74700528..74700940
ENCFF002CKX	POLR2A	16:74700559..74700890
ENCFF002CLM	POLR2A	16:74700478..74701018
ENCFF002CMI	POLR2A	16:74700204..74700960
ENCFF002CMI	POLR2A	16:74701274..74701636
ENCFF002COJ	POLR2A	16:74700559..74700995
ENCFF002CPG	POLR2A	16:74700569..74700830
ENCFF002CPH	POLR2A	16:74700542..74700932
ENCFF002CQA	POLR2A	16:74700542..74700879
ENCFF002CQC	POLR2A	16:74700553..74700886
ENCFF002CQE	POLR2A	16:74700586..74700890
ENCFF002CQG	POLR2A	16:74700620..74700889
ENCFF002CQI	POLR2A	16:74700592..74700878
ENCFF002CQK	POLR2A	16:74700581..74700923
ENCFF002CQM	POLR2A	16:74700573..74700883
ENCFF002CQO	POLR2A	16:74700546..74700914
ENCFF002CRK	POLR2A	16:74700508..74701032
ENCFF002CRO	POLR2A	16:74700493..74700913
ENCFF002CSY	POLR2A	16:74700203..74700988
ENCFF002CUP	POLR2A	16:74700615..74700884
ENCFF002CUQ	POLR2A	16:74700542..74700897
ENCFF002CVF	POLR2A	16:74700510..74700926
ENCFF002CVJ	POLR2A	16:74700551..74700918
ENCFF002CXM	POLR2A	16:74700608..74700774
ENCFF002CXN	POLR2A	16:74700611..74700760
ENCFF002CXO	POLR2A	16:74700600..74700851
ENCFF002CXO	POLR2A	16:74701183..74701607
ENCFF002CXP	POLR2A	16:74700552..74700873
ENCFF002CXR	POLR2A	16:74700572..74700905
ENCFF002CZC	POLR2A	16:74700569..74700965
ENCFF002CZD	POLR2A	16:74700584..74700973
ENCFF002CZQ	POLR2A	16:74700572..74700899
ENCFF002CZW	POLR2A	16:74700420..74701020
ENCFF002CZW	POLR2A	16:74700420..74701023
ENCFF002CZY	POLR2A	16:74700563..74700902
ENCFF002DAE	POLR2A	16:74700568..74700878
ENCFF002DAH	POLR2A	16:74700659..74700778
ENCFF002DAK	POLR2A	16:74700480..74700980
ENCFF002DAS	POLR2A	16:74700479..74700955
ENCFF002DAS	POLR2A	16:74701281..74701757
ENCFF002DAV	POLR2A	16:74700630..74700832
ENCFF002DAY	POLR2A	16:74700335..74700971
ENCFF002DBB	POLR2A	16:74700630..74700830
ENCFF002DBE	POLR2A	16:74700577..74700876
ENCFF002DBO	POLR2A	16:74700565..74700858
ENCFF002DBP	POLR2A	16:74700592..74700841
ENCFF002DBQ	POLR2A	16:74700619..74700792
ENCFF002DBT	POLR2A	16:74700552..74700922

EST

No EST(s) were mapped for retro_hsap_1652 retrocopy.

TSS

No TSS is located nearby retro_hsap_1652 retrocopy 5' end.

Lab

retro_hsap_1652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1652 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1123
Gorilla gorilla	retro_ggor_1247
Pongo abelii	retro_pabe_1365

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000120802	1 retrocopy	retro_hsap_1652 ,
Gorilla gorilla	ENSGGOG00000003388	1 retrocopy	retro_ggor_1247,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.17 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.42 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.19 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.15 RPM
FIN_HG00377	0.38 RPM
FIN_HG00378	0.28 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.32 RPM
GBR_HG00114	0.32 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.16 RPM
GBR_HG00142	0.28 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.53 RPM
TSI_NA20518	0.33 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.23 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.24 RPM
TSI_NA20798	0.25 RPM
YRI_NA18870	0.14 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.17 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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