RetrogeneDB ID: retro_hsap_1761

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:45501195..45502239(+)
• Located in intron of: ENSG00000178852

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NFE2L3
• Ensembl ID: ENSG00000050344
• Aliases: NFE2L3, NRF3
• Description: nuclear factor (erythroid-derived 2)-like 3 [Source:HGNC Symbol;Acc:7783]

Sequence

>retro_hsap_1761
AGCTTTGCTGGGCTCCGTGTAGACCTAGACCTTTACCTGCTACTGCCGCCGCCCACCCTGCTCCGGGACGAGCTGCTGTT
CCTGGGCGGCCCGGCCAGCTCCGTCTACGCGCTCAGCCCCTTCTCGGCCTCGGGAGGGAGGGGGCGCGCGGGCCAGTTGC
ACCCCAAGGGCCGGGAGCTGGACTCTGCCGCGCCGCCCGAGGGCCCGCTGCTCCGGGAGGTGCGCGCTCGGGGTCCCCTT
CATCCCTCTCACCCCGGTGGATGCGTGGCTGGTGCACAGCGTGGCTGCCAGGAGAGCGGACGAGGCCCACGGGCTGCTCG
GCGCCGCCGCCGCCTAGTCCACCGGAGGAGCCGGCGCCAGCGTGGACGGCGGCAGCCAGGCTGTGCAGGGGGGCTGCGGG
GACTCCCGAGCGGCTCGGAGTGGCCCCTTGGACGCCGGGGAAGAGGAGAAGGCACCCGCGGAACCGACGGCTCAGGTGCC
GGACGCTGGCGGATGTGCGAGCGGGGAGAACGAGGTACTAAGAGAAAAGCACGAAGCTGTGGATCATAGTTCCCAGCGTG
AGGAAAATGAAGAAAGGGTGTCAGCCCAGAAGGAGAACTCACTTCAGCAGAATAATGATGATGAAAACAAAATAGCAGAG
GAACCTGATTGGGAGGCAGAAAAGACCACTGAATCTAGAAATGAGAGACATCTGAATGGGACAGATACTTATTTCTCTCT
GGAAGACTTATTCCAGTTGCTTTCATCACAGCCTGAAAATTCACGGAGGGCTTCTCATTGGGAGATATTCCTCTTCCAGG
CAGTATCAGTGATGGCATGAATTCTTCAGCACATTATCACGTAAACTTCAGCCAGGCTATAAGTCATGATGTGAATCTTC
ATGAGGCCATCTTGCTTTGTGCCAACAGTACATTTAGAAGAGATCCAATAGCAAGGACTTCACAGTCACAAGAACCGTTT
CTAAAGTTAAATTCTCATACCACCAATCCTGAGCAAACCCTTCCTGGAACTAATTTGACAGGATTTCTTTCTCCGGTTGA
CAAT

Alignment

ORF - retro_hsap_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLAGLRVDLDLYLLLPPPTLLQDELLFLGGPASSAYALSPFSASGGWGRAGHLHPKGRELDPAAPPEGQL
          S.AGLRVDLDLYLLLPPPTLL.DELLFLGGPASS.YALSPFSASGG.GRAG.LHPKGRELD.AAPPEG.L
Retrocopy SFAGLRVDLDLYLLLPPPTLLRDELLFLGGPASSVYALSPFSASGGRGRAGQLHPKGRELDSAAPPEGPL

Parental  LREVRALGVPFVPR-TSVDAWLVHSVAAGSADEAHGLLGAAAASSTGGAGASVDGGSQAVQGGGGDPRAA
          LREVRA.G.P..P..T.VDAWLVHSVAA..ADEAHGLLGAAAA.STGGAGASVDGGSQAVQGG.GD.RAA
Retrocopy LREVRARG-PLHPS>TPVDAWLVHSVAARRADEAHGLLGAAAA*STGGAGASVDGGSQAVQGGCGDSRAA

Parental  RSGPLDAGEEEKAPAEPTAQVPDAGGCASEENGVLREKHEAVDHSSQHEENEERVSAQKENSLQQNDDDE
          RSGPLDAGEEEKAPAEPTAQVPDAGGCAS.EN.VLREKHEAVDHSSQ.EENEERVSAQKENSLQQN.DDE
Retrocopy RSGPLDAGEEEKAPAEPTAQVPDAGGCASGENEVLREKHEAVDHSSQREENEERVSAQKENSLQQNNDDE

Parental  NKIAEKPDWEAEKTTESRNERHLNGTDTSFSLEDLFQLLSSQPENS-LEGISLGDIPLPGSISDGMNSSA
          NKIAE.PDWEAEKTTESRNERHLNGTDT.FSLEDLFQLLSSQPENS..EG.SLGDIPLPGSISDGMNSSA
Retrocopy NKIAEEPDWEAEKTTESRNERHLNGTDTYFSLEDLFQLLSSQPENS<TEGFSLGDIPLPGSISDGMNSSA

Parental  HYHVNFSQAISQDVNLHEAILLCPNNTFRRDPTARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLSPVD
          HYHVNFSQAIS.DVNLHEAILLC.N.TFRRDP.ARTSQSQEPFL.LNSHTTNPEQTLPGTNLTGFLSPVD
Retrocopy HYHVNFSQAISHDVNLHEAILLCANSTFRRDPIARTSQSQEPFLKLNSHTTNPEQTLPGTNLTGFLSPVD

Parental  N
          N
Retrocopy N

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	0.83 RPM	14.55 RPM
bodymap2_adrenal	0.66 RPM	28.41 RPM
bodymap2_brain	0.09 RPM	6.73 RPM
bodymap2_breast	0.43 RPM	8.19 RPM
bodymap2_colon	0.83 RPM	6.13 RPM
bodymap2_heart	0.20 RPM	7.27 RPM
bodymap2_kidney	0.95 RPM	15.26 RPM
bodymap2_liver	0.17 RPM	5.56 RPM
bodymap2_lung	0.18 RPM	19.02 RPM
bodymap2_lymph_node	1.90 RPM	18.71 RPM
bodymap2_ovary	0.75 RPM	6.00 RPM
bodymap2_prostate	1.84 RPM	7.60 RPM
bodymap2_skeletal_muscle	0.02 RPM	2.42 RPM
bodymap2_testis	0.28 RPM	5.96 RPM
bodymap2_thyroid	0.60 RPM	5.88 RPM
bodymap2_white_blood_cells	0.10 RPM	18.47 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1761 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	17:45500799..45501032
ENCFF002CFX	POLR2A	17:45500791..45501023
ENCFF002CGN	POLR2A	17:45500685..45501149

EST

No EST(s) were mapped for retro_hsap_1761 retrocopy.

TSS

No TSS is located nearby retro_hsap_1761 retrocopy 5' end.

Lab

retro_hsap_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1761 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000050344	1 retrocopy	retro_hsap_1761 ,
Pongo abelii	ENSPPYG00000017716	1 retrocopy	retro_pabe_1571,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.43 RPM
CEU_NA11843	0.68 RPM
CEU_NA11930	0.88 RPM
CEU_NA12004	0.53 RPM
CEU_NA12400	0.91 RPM
CEU_NA12751	0.41 RPM
CEU_NA12760	0.45 RPM
CEU_NA12827	0.90 RPM
CEU_NA12872	0.41 RPM
CEU_NA12873	0.51 RPM
FIN_HG00183	0.60 RPM
FIN_HG00277	0.78 RPM
FIN_HG00315	1.08 RPM
FIN_HG00321	0.85 RPM
FIN_HG00328	0.43 RPM
FIN_HG00338	0.36 RPM
FIN_HG00349	0.60 RPM
FIN_HG00375	0.68 RPM
FIN_HG00377	0.43 RPM
FIN_HG00378	0.42 RPM
GBR_HG00099	0.32 RPM
GBR_HG00111	0.92 RPM
GBR_HG00114	0.97 RPM
GBR_HG00119	0.84 RPM
GBR_HG00131	0.55 RPM
GBR_HG00133	0.84 RPM
GBR_HG00134	1.03 RPM
GBR_HG00137	0.80 RPM
GBR_HG00142	0.67 RPM
GBR_HG00143	0.70 RPM
TSI_NA20512	0.96 RPM
TSI_NA20513	1.26 RPM
TSI_NA20518	0.56 RPM
TSI_NA20532	1.53 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	0.68 RPM
TSI_NA20771	0.40 RPM
TSI_NA20786	0.24 RPM
TSI_NA20798	0.94 RPM
YRI_NA18870	0.68 RPM
YRI_NA18907	0.62 RPM
YRI_NA18916	0.61 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.27 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.58 RPM
YRI_NA19213	0.50 RPM
YRI_NA19214	0.30 RPM
YRI_NA19223	1.23 RPM

---

Indel association:

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