RetrogeneDB ID: retro_hsap_2989

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:146377156..146377990(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000248745
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NMNAT1
• Ensembl ID: ENSG00000173614
• Aliases: NMNAT1, LCA9, NMNAT, PNAT1
• Description: nicotinamide nucleotide adenylyltransferase 1 [Source:HGNC Symbol;Acc:17877]

Sequence

>retro_hsap_2989
ATGGAAAATTCAGAGACTGAAGTGGTTCTCCTTGCTGTAGCTCCTTCAATCCTATCACCAACAGGCACCTAAGGTTGTTT
GAGCTGGCCAAGGACTATATGAATGGAACAGGAAGATATAGAGTTGTCAAACACATGATCTTTCCTGTTGGTGATGCTTA
TAAGAAGAAAGGACTCATTCCTGCCCATCACCAGGTCATCATAGCCGAACTTGCCACCAAGAATTCCAAGTGAGTGGAAG
TTGATACATGGGAAAGTCTTCAGAAAAAGTGGAAAGAGACTATTACTTTGCTAACACACCATCAGGAGAAACTGGAGGCT
ACTAACTGTGATCACAAGCAGAACTCACCTACACTAGAAAGGCCTGGATGGAAGAGGAAGAGAACTGAACAAAGACAAGA
TTCTACTAAAAAAAAAATCCCTAGAGCCAAAACCAAAAGGTGCATCAAAGGTCAAGCTGCTGTGTGGGGCAGATTTACTG
GAGTGCTTTGGTGTTCCTAATTTGTGGAAAGGTGAAAACATCACCCAAACTGTGGCTGACTATGGGCTCTTATGTATTAC
TTGGGCTGCAAATGATGCTCACAAATTCATCTATGACTCTAATGTGCTATGGAAACACCACAGCAACATTCATGTGGTGA
ATGAATGGATCACTAATGATATCTCATCCACAAAAATCCAGAGAGCCCTTAGAAGGGGCCAGAGCGTTCACTACTTGCTA
CCAGATCTTTTTCAAGAATACATCGAAAAGCATAATTTGTACAGCTCTGAGAGTGAAGACAGGAATGCTAGGGTCATGTT
GGCCCCTTTGTAGAGAAATATTGCAGAAGCTAAG

Alignment

ORF - retro_hsap_2989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.72 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENSEKTEVVLLA-CGSFNPITNMHLRLFELAKDYMNGTGRYTVVKGIISPVGDAYKKKGLIPAYHRVIM
          MENSE.TEVVLLA.C.SFNPITN.HLRLFELAKDYMNGTGRY.VVK..I.PVGDAYKKKGLIPA.H.VI.
Retrocopy MENSE-TEVVLLA<CSSFNPITNRHLRLFELAKDYMNGTGRYRVVKHMIFPVGDAYKKKGLIPAHHQVII

Parental  AELATKNSKWVEVDTWESLQKEWKETLKVLRHHQEKLEASDCDHQQNSPTLERPGRKRKWTET-QDSSQK
          AELATKNSK.VEVDTWESLQK.WKET...L.HHQEKLEA..CDH.QNSPTLERPG.KRK.TE..QDS...
Retrocopy AELATKNSK*VEVDTWESLQKKWKETITLLTHHQEKLEATNCDHKQNSPTLERPGWKRKRTEQRQDSTXX

Parental  K-SLEPKTKAVPKVKLLCGADLLESFAVPNLWKSEDITQIVANYGLICVTRAGNDAQKFIYESDVLWKHR
          ..SLEPK.K...KVKLLCGADLLE.F.VPNLWK.E.ITQ.VA.YGL.C.T.A.NDA.KFIY.S.VLWKH.
Retrocopy X>SLEPKPKGASKVKLLCGADLLECFGVPNLWKGENITQTVADYGLLCITWAANDAHKFIYDSNVLWKHH

Parental  SNIHVVNEWIANDISSTKIRRALRRGQSIRYLVPDLVQEYIEKHNLYSSESEDRNAGVILAPLQRNTAEA
          SNIHVVNEWI.NDISSTKI.RALRRGQS..YL.PDL.QEYIEKHNLYSSESEDRNA.V.LAPL.RN.AEA
Retrocopy SNIHVVNEWITNDISSTKIQRALRRGQSVHYLLPDLFQEYIEKHNLYSSESEDRNARVMLAPL*RNIAEA

Parental  K
          K
Retrocopy K

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	8.65 RPM
bodymap2_adrenal	0.00 RPM	7.82 RPM
bodymap2_brain	0.00 RPM	7.74 RPM
bodymap2_breast	0.00 RPM	13.44 RPM
bodymap2_colon	0.00 RPM	10.81 RPM
bodymap2_heart	0.00 RPM	14.88 RPM
bodymap2_kidney	0.00 RPM	19.42 RPM
bodymap2_liver	0.00 RPM	5.13 RPM
bodymap2_lung	0.00 RPM	3.96 RPM
bodymap2_lymph_node	0.00 RPM	8.39 RPM
bodymap2_ovary	0.00 RPM	13.40 RPM
bodymap2_prostate	0.00 RPM	9.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.42 RPM
bodymap2_testis	0.00 RPM	12.86 RPM
bodymap2_thyroid	0.00 RPM	14.74 RPM
bodymap2_white_blood_cells	0.00 RPM	9.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2989 was not detected

EST

No EST(s) were mapped for retro_hsap_2989 retrocopy.

TSS

No TSS is located nearby retro_hsap_2989 retrocopy 5' end.

Lab

retro_hsap_2989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001361	2 retrocopies	retro_btau_1153, retro_btau_1654,
Callithrix jacchus	ENSCJAG00000005483	1 retrocopy	retro_cjac_1690,
Homo sapiens	ENSG00000173614	3 retrocopies	retro_hsap_247, retro_hsap_2740, retro_hsap_2989 ,
Macaca mulatta	ENSMMUG00000005863	2 retrocopies	retro_mmul_1488, retro_mmul_446,
Nomascus leucogenys	ENSNLEG00000009375	2 retrocopies	retro_nleu_1072, retro_nleu_741,
Oryctolagus cuniculus	ENSOCUG00000023212	1 retrocopy	retro_ocun_1243,
Otolemur garnettii	ENSOGAG00000033037	2 retrocopies	retro_ogar_1088, retro_ogar_637,

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	0.00 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	0.03 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).