RetrogeneDB ID: retro_hsap_438

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:117075699..117076714(-)
• Located in intron of: ENSG00000116815

Retrocopy information

• Ensembl ID: ENSG00000177173
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSG00000205531
• Aliases: NAP1L4, NAP1L4b, NAP2, NAP2L, hNAP2
• Description: nucleosome assembly protein 1-like 4 [Source:HGNC Symbol;Acc:7640]

Sequence

>retro_hsap_438
ATGGCAGATAACAGTTTTTCAGATGGGGTTCCTTCAGATTTCGTGGAAGCTGCTAAAAATGCAAGTAAGACGGAAAAGCT
CACGGATCAGGTGATGCAGAATCCTGGAGTTTTGGCAGCTTTACAGGAGCGACTTGACAATGCCCCTCACACCCCTTCCA
GCTACATCGAAACTTTACCTAAAGCAGTAAAAAGAAGAATTAATGCATTGAAACAAATTCAGGTGAGATGCGCTCATATA
GAAGCCAAGTTCTATGAAGAAGTTCATGACTTGGAAAGAAAATATGCAGCATTATACCAGCCTCTCTTTGACGAGAGAAG
AGAATTTATCACCGGTGATGTTGAACCAACATCTGATATGGAATCAGAATGGCACCGTGAAAATGAAGAGGAGGAGAAAT
TGGCTGGAGACAGGAAAAATAAAGTAGTCATAACAGAAAAAGCAGCAGCAACAGCTGAAGAGCCAAATCCCAAAGGAATT
CCAGAGTTCTGGTTTACCATCTTTAGAAATGTAGATATGCTAAGTGAATTAGTCCAGGAATATGATGAACCAATCTTGAA
ATACCTGCAGGATATTAAAGTGAAGTTTTCTGACCCTGGACAGCCTATGTCTTTCATATTAAGAGTTCCACTTTCAACCC
AATGACTGCTTTGCCAACTCAGTCCTGACAAAAACCTGCAAGATGAAATCAGAACCAGATAAGGCTGATCCCTTTTCATT
TGCAGGTCCTGAGATCATGGACTGCGATGGGTGTACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCATCA
AGAAAAAGCAGAAGCGTAAGGGTCCAGGCACTGTTAGAACAATTACCAAACAAGTATCCAATGAGTCATTTTTCAACTTC
TTCAATCCACTGAAAGCATCTGGGGACGGAGAATCACTGGATAAAGATTCTGAATTCGTATTAGCCTCTGATTTTGAAAT
TGGACACTTTTTCCGTGAGCGGACCACAGGCTGTGCTGTACTTCGCTGGGGAGGC

Alignment

ORF - retro_hsap_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 89.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADHSFSDGVPSDSVEAAKNASNTEKLTDQVMQNPRVLAALQERLDNVPHTPSSYIETLPKAVKRRINAL
          MAD.SFSDGVPSD.VEAAKNAS.TEKLTDQVMQNP.VLAALQERLDN.PHTPSSYIETLPKAVKRRINAL
Retrocopy MADNSFSDGVPSDFVEAAKNASKTEKLTDQVMQNPGVLAALQERLDNAPHTPSSYIETLPKAVKRRINAL

Parental  KQLQVRCAHIEAKFYEEVHDLERKYAALYQPLFDKRREFITGDVEPT-DAESEWHSENEEEEKLAGDMKS
          KQ.QVRCAHIEAKFYEEVHDLERKYAALYQPLFD.RREFITGDVEPT.D.ESEWH.ENEEEEKLAGD.K.
Retrocopy KQIQVRCAHIEAKFYEEVHDLERKYAALYQPLFDERREFITGDVEPTSDMESEWHRENEEEEKLAGDRKN

Parental  KVVVTEKAAATAEEPDPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSFVL-EF
          KVV.TEKAAATAEEP.PKGIPEFWFTIFRNVDMLSELVQEYDEPILK.LQDIKVKFSDPGQPMSF.L.EF
Retrocopy KVVITEKAAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKYLQDIKVKFSDPGQPMSFIL>EF

Parental  HFEPNDYFTNSVLTKTYKMKSEPDKADPFSFEGPEIVDCDGCTIDWKKGKNVTVKTIKKKQKHKGRGTVR
          HF.PND.F.NSVLTKT.KMKSEPDKADPFSF.GPEI.DCDGCTIDWKKGKNVTVKTIKKKQK.KG.GTVR
Retrocopy HFQPNDCFANSVLTKTCKMKSEPDKADPFSFAGPEIMDCDGCTIDWKKGKNVTVKTIKKKQKRKGPGTVR

Parental  TITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLASDFEIGHFFRERIVPRAVLYFTG
          TITKQV.NESFFNFFNPLKASGDGESLD.DSEF.LASDFEIGHFFRER....AVL...G
Retrocopy TITKQVSNESFFNFFNPLKASGDGESLDKDSEFVLASDFEIGHFFRERTTGCAVLRWGG

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	0.16 RPM	67.35 RPM
bodymap2_adrenal	0.43 RPM	61.14 RPM
bodymap2_brain	0.07 RPM	100.30 RPM
bodymap2_breast	0.25 RPM	76.32 RPM
bodymap2_colon	0.12 RPM	67.52 RPM
bodymap2_heart	0.30 RPM	100.32 RPM
bodymap2_kidney	0.17 RPM	87.83 RPM
bodymap2_liver	0.11 RPM	33.65 RPM
bodymap2_lung	0.56 RPM	65.95 RPM
bodymap2_lymph_node	0.31 RPM	105.84 RPM
bodymap2_ovary	0.13 RPM	91.64 RPM
bodymap2_prostate	0.14 RPM	95.07 RPM
bodymap2_skeletal_muscle	0.00 RPM	141.30 RPM
bodymap2_testis	0.06 RPM	156.31 RPM
bodymap2_thyroid	0.19 RPM	94.82 RPM
bodymap2_white_blood_cells	0.10 RPM	98.77 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_438 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	1:117076681..117076999
ENCFF002CIO	POLR2A	1:117076729..117077005

EST

1 EST(s) were mapped to retro_hsap_438 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
R19751	117075770	117076265	97.8	485	1	476

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_81037	1337 libraries	472 libraries	19 libraries	0 libraries	1 library

The graphical summary, for retro_hsap_438 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_438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_438 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_192
Gorilla gorilla	retro_ggor_423
Pongo abelii	retro_pabe_288

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Homo sapiens	ENSG00000205531	1 retrocopy	retro_hsap_438 ,
Gorilla gorilla	ENSGGOG00000013223	1 retrocopy	retro_ggor_423,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,