RetrogeneDB ID: retro_hsap_3712

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:27087787..27088244(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NHP2
• Ensembl ID: ENSG00000145912
• Aliases: NHP2, DKCB2, NHP2P, NOLA2
• Description: NHP2 ribonucleoprotein [Source:HGNC Symbol;Acc:14377]

Sequence

>retro_hsap_3712
ATGACCAAAATAAAGGTAGATTCGATGGGCCCGAGGCTCAGGAGGAGGCGTGCTCCGGGGAGCGCACCTACCAGGAGCTG
CTGGTTAACCAGAACCCCATCGTGCAGCCCCTGGCTTCTCGCCGCCTCACGCGGAACCTCTACAAATGCATCAAGAAAGC
CATGAAGCAGAAGCAGCTTCGGCGCGGGGTGAAAGAGGTTCAGAAATTTGTCAACAAAGGAGAAAAAGGGATCATGGTTT
TGGCAGAAGACACACTGCCCATTGAGGTATACTGCCATCTTCCAGTCATGTGTGAGGACCGAAATCTGGCCTATGTCTCT
ATCCCTCTAAGATGAACCTGGGTGCAGCCGCAGGCTCCAAGTGCCCCACCTGTGTGATAATGGTCAAGCCCCACAAGGAG
TACCAGGAGGCCTACGACAAGTGCCTGGAGGAGGTGCAGTCCCTACCCCTACCCCTA

Alignment

ORF - retro_hsap_3712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTKIKADP-DGPEAQAEACSGERTYQELLVNQNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQK
          MTKIK.D..DGPEAQ.EACSGERTYQELLVNQNPI.QPLASRRLTR.LYKCIKKA.KQKQ.RRGVKEVQK
Retrocopy MTKIKVDS<DGPEAQEEACSGERTYQELLVNQNPIVQPLASRRLTRNLYKCIKKAMKQKQLRRGVKEVQK

Parental  FVNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYI-PSKTDLGAAAGSKRPTCVIMVKPHEEYQEA
          FVNKGEKGIMVLA.DTLPIEVYCHLPVMCEDRNL.YV.I.PSK..LGAAAGSK.PTCVIMVKPH.EYQEA
Retrocopy FVNKGEKGIMVLAEDTLPIEVYCHLPVMCEDRNLAYVSI<PSKMNLGAAAGSKCPTCVIMVKPHKEYQEA

Parental  YDECLEEVQSLPLPL
          YD.CLEEVQSLPLPL
Retrocopy YDKCLEEVQSLPLPL

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	18.80 RPM
bodymap2_adrenal	0.00 RPM	22.56 RPM
bodymap2_brain	0.00 RPM	15.70 RPM
bodymap2_breast	0.00 RPM	13.15 RPM
bodymap2_colon	0.00 RPM	19.34 RPM
bodymap2_heart	0.00 RPM	9.54 RPM
bodymap2_kidney	0.00 RPM	18.94 RPM
bodymap2_liver	0.00 RPM	13.03 RPM
bodymap2_lung	0.00 RPM	14.47 RPM
bodymap2_lymph_node	0.00 RPM	14.51 RPM
bodymap2_ovary	0.00 RPM	20.20 RPM
bodymap2_prostate	0.00 RPM	24.77 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.53 RPM
bodymap2_testis	0.00 RPM	19.64 RPM
bodymap2_thyroid	0.00 RPM	19.02 RPM
bodymap2_white_blood_cells	0.00 RPM	16.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3712 was not detected

EST

No EST(s) were mapped for retro_hsap_3712 retrocopy.

TSS

No TSS is located nearby retro_hsap_3712 retrocopy 5' end.

Lab

retro_hsap_3712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3712 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2509

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712 , retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,

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	0.05 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).