RetrogeneDB ID: retro_hsap_3692

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:1654241..1654965(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSG00000108064
• Aliases: TFAM, MTTF1, MTTFA, TCF6, TCF6L1, TCF6L2, TCF6L3
• Description: transcription factor A, mitochondrial [Source:HGNC Symbol;Acc:11741]

Sequence

>retro_hsap_3692
AGCACGTGGGGTGTGCTGAGGGCCCTGGGAAGGTCCTGGCGGAGCTGTGTACCAGCTGTGGAAGTCGACCGCGCTTCCCC
TTCAGTTTTATGTATTTATGGAAATGGTTTTCGCCTGTCTTGGCAAGTTATCCAAAGAAACCTGTAACTTCTTACCTTTG
ATTTTCTAAAGAACAACTACCCATATTTAAAGCTCAGAACCCAGATGCAAAAAATACAGAACTAATTAGAAGAATCGCTG
AGCATTGGACGGAACTTCCCAATTCAGAGAAAAAAAATATATGAAGATGCTTATAGGGTGGACTGGCAGGCATACAAAGA
AGAGATAAGCAGAATTCAAGAACAGCTAACTCCAAGTCAGATTATGTCTTTGGAAAAAGAAATCATGCAGGAACATTTAA
AAAGGAAAGCTTTAATAAAAAAGAGAGTTAACACTGCTTGGAAAACCAAAATGATCTCGTTCAGCTTATAACATTTATGT
AGCTGAAAGCTTCCAAGAAGCTAAGGATGGTTCACCGCAGGCAAAGCTGAAGACTGTAAATGAAAACTGGAAAAATCTGT
CTGGTTCTCAAAAGAAAGTATATATTCAACTTGCTAAAGATGATAAAATTCATTATTATAATGAAATGAAGTCTTGGGAA
GAACAAATGATTGAAGTTGGACGAAAGGATTTTCTACGTCGCAAAATAAAGCAACCACCTTTAAAAGATGGCACTGAGAA
GTGT

Alignment

ORF - retro_hsap_3692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.76 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SMWGVLSALGRSG-AELCTGCGSRLRSPFSFVYLPRWFSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD
          S.WGVL.ALGRS..AELCT.CGSR.R.PFSF.YL..WFS.VLAS.PKKPV.SYL.FSKEQLPIFKAQNPD
Retrocopy STWGVLRALGRSW<AELCTSCGSRPRFPFSFMYLWKWFSPVLASYPKKPVTSYL*FSKEQLPIFKAQNPD

Parental  AKTTELIRRIAQRWRELPDSKKKI-YQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHL-KRKA
          AK.TELIRRIA..W.ELP.S.....Y.DAYR..WQ.YKEEISR..EQLTPSQIMSLEKEIM..HL.K...
Retrocopy AKNTELIRRIAEHWTELPNSEXXX>YEDAYRVDWQAYKEEISRIQEQLTPSQIMSLEKEIMQEHL<KKES

Parental  MTKK-KELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRY
          ..KK..ELTLLGKPK..RSAYN.YVAE.FQEAK..SPQ.KLKTV.ENWKNLS.S.K..YIQ.AK.D...Y
Retrocopy FNKK<RELTLLGKPK*SRSAYNIYVAESFQEAKDGSPQAKLKTVNENWKNLSGSQKKVYIQLAKDDKIHY

Parental  HNEMKSWEEQMIEVGRKDLLRRTIKK-QRKYGAEEC
          .NEMKSWEEQMIEVGRKD.LRR.IK....K.G.E.C
Retrocopy YNEMKSWEEQMIEVGRKDFLRRKIKQPPLKDGTEKC

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	0.08 RPM	40.83 RPM
bodymap2_adrenal	0.00 RPM	56.88 RPM
bodymap2_brain	0.09 RPM	32.98 RPM
bodymap2_breast	0.10 RPM	47.22 RPM
bodymap2_colon	0.00 RPM	41.51 RPM
bodymap2_heart	0.00 RPM	31.64 RPM
bodymap2_kidney	0.00 RPM	52.98 RPM
bodymap2_liver	0.00 RPM	33.52 RPM
bodymap2_lung	0.00 RPM	27.13 RPM
bodymap2_lymph_node	0.00 RPM	35.69 RPM
bodymap2_ovary	0.15 RPM	61.84 RPM
bodymap2_prostate	0.00 RPM	41.05 RPM
bodymap2_skeletal_muscle	0.00 RPM	19.06 RPM
bodymap2_testis	0.13 RPM	74.11 RPM
bodymap2_thyroid	0.13 RPM	68.11 RPM
bodymap2_white_blood_cells	0.00 RPM	76.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3692 was not detected

EST

No EST(s) were mapped for retro_hsap_3692 retrocopy.

TSS

No TSS is located nearby retro_hsap_3692 retrocopy 5' end.

Lab

retro_hsap_3692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3692 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692 , retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,

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	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 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	0.02 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	0.02 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

---

Indel association:

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