RetrogeneDB ID: retro_hsap_4064

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:61850265..61852430(-)
• Located in intron of: ENSG00000254777

Retrocopy information

• Ensembl ID: ENSG00000255397
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NASP
• Ensembl ID: ENSG00000132780
• Aliases: NASP, FLB7527, PRO1999
• Description: nuclear autoantigenic sperm protein (histone-binding) [Source:HGNC Symbol;Acc:7644]

Sequence

>retro_hsap_4064
ATGGCCACGGAGTCCACAGCCACTGCCGCCATCGCTGCGGAGCTGGTTTCTGCCAACAAAATTGAAGATGTTCCTGCTCC
TTCTACATCTGCAGATAAAGTGGAGAGAATCGAGAATGGTGTATTGGGAAACACCTTGGATGGTGTGCATGTGGAAGAGG
AAGAAGGAGAAAAAACAGAAGATGAATCTCTGGTAGAAAATAATGATAGCATAGATGAGGAAGCAAGGAAAGAGTTGAGA
GAACAGGTTTATGACTCCATGGGAGAAAAAGAAGAAGCCAAAAAAACAGAAGACAAGTCTTTCGCAAAGCCTGAAACTGA
TAAAGAACAGGACTGTGAAATGGAGAAGGGTGGAAGAGAAGATATGGATATAAGTGAATCTGCAGAGGAGCCACAGGAAA
AAGTTGACTTGACTCTAGGTTGGTTAACTGAAATCTCTGAAGGGGCAAAAGGAGGAGGAGCACCAGAAGGACCAAATGAA
GCTGAGGTCACTTCTGGGAAGCCAGAACAGGAAGTACCAGATGTTGAGGAAGAAAAATCAGTTTCTGAAACTGATGTCCA
AGAAGAGTGCAGAGAAAAGGAGGTTGGGAGAAGCACAGAGAGGTAATTGTGAGCATAGAGGAGAAGCCAAAAGAAGTTTC
AGAAGAGCAGACTGTGGTGATTCTAGAAAAGCAGGGCACTGCAGTGGAGGTAGCAGCAGAGTCTTTAGACCCAACAGTCA
AGCCAGTAGATGTGGGTGGGGACGAGCCAGAGGAGAAGGTAGTTACCTCTGAAAAGGCAGGAAAGGTGGTTCTTGAGTAA
CTGGTAGGTCAAGAAGTGCCACCTGCTGAAGAGTCACCGGAGGTGACAACAGAGGCTGCAGAGGCCTCAGCCTTAGAGGC
TGGATCAGAAGTCTCTGAAAAGCCTGGGCAGGAGGCTACAGTTCTCCCTAAGGATGGTGCGGTCAATGGACCGTCAGCTG
TAGGAGATCAGACTCCTACTGAACCACAGACTTCTATAGAAAGACTGACAGAAACAAAAGATGGCTCAGGACTAGAGGAG
AAGGTCAGAGCAAAGCTGGTTCCTAGTCAGGAGGAGACTAAGCTGTCTGTAGAAGAGTCTGAGGCAGCTGGAGATGGGGT
TGATACCAAGGTAGCCCAGGGAGCTACTGAGAAATCACCTGAAGACAAAGTTCAGATAGCTGCTAATGAAGAGACAAAAG
AGAGAGGACGAACAGATAAAAGAGGGTGAAGAAACTGAAGGCTTGGAAGAGGATGATAAAGAAAATGATAAGGCTGAAGA
AATGCCAAATGATTCAGTCCTTGAAAACAAGTCTCTTCAAGAAAATGAAGAGGAGGAGATTGGGAACCTAGAGCTTGCCT
GGGATACACTGGATTTAGCAAAGATCGTTTTTAAAAGGCAAGAAACAAAAGCCCAGCTTTATGTTGCCCAGGCACATCTT
AAACTCGGAGAAGTTGGTGTTGAATCTGAAAACTATGTGCAAGCTGTGGAGGAGTTCCAGTCCTGCCTAAACCTGTAGGA
ACAGTACCTGGAAGCCTACGACCATCTCCTTGCAGAGACCCACTACCAGCTGGGCTTGGCTTATGGGTACAACTTTCAGT
ATGATGAGGCAGTGGCACAGTTCAGCAAATCTATTGAAGTCATTGAGAAGAGAATGGCTGTACTAAACGAGCAGGTGAAG
GAGGCTGAAGGATCGTCTGCTGAATACAAGAAAGAAATTGAGGAACTGAAGGAACTGCTACCCGAAATTACAGAAAAGAC
AGAAGATGCAAAGGAGTCTCAGACTACTGGGAATGTAGCTGAACTGGCTCTGAAAGCTACTCTGGTGGAGAGCTCTACTT
CAGGTTTCACTCCTAGTGGAGGAGGCTCTTCAGTCTCCTGATTGCCAGTAGAAAGCCAACAGATGGTGCTTCCTCATCAA
ATTGTGTGACTGATATTTCTCACTTTGTCAGAAAGAAGAGGAAACCGGAGGAACAGAGTCCCTGGAAAGATGATGCAAAG
AAAGTCAAACAAGAGCTGGAGGTGAACGGAGGCAGTGGAGATGCTGTCCCCAGTGGAAATGAAGTTTTGGAAAACATGGA
GGAGGAGGCTGAGAATCGGGTTGAAAGCCGGGCGGCAGTGGAGGGGACAGTGGAGGCTGGAGCTACAGCTGAAAGCACTG
CATGT

Alignment

ORF - retro_hsap_4064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAMESTATAAVAAELVSADKIEDVPAPSTSADKVERMENGVLGNALEGVHVEEEEGEKTEDESLVENNDN
          MA.ESTATAA.AAELVSA.KIEDVPAPSTSADKVER.ENGVLGN.L.GVHVEEEEGEKTEDESLVENND.
Retrocopy MATESTATAAIAAELVSANKIEDVPAPSTSADKVERIENGVLGNTLDGVHVEEEEGEKTEDESLVENNDS

Parental  IDEEAREELREQVYDAMGEKEEAKKTEDKSLAKPETDKEQDSEMEKGGREDMDISKSAEEPQEKVDLTLD
          IDEEAR.ELREQVYD.MGEKEEAKKTEDKS.AKPETDKEQD.EMEKGGREDMDIS.SAEEPQEKVDLTL.
Retrocopy IDEEARKELREQVYDSMGEKEEAKKTEDKSFAKPETDKEQDCEMEKGGREDMDISESAEEPQEKVDLTLG

Parental  WLTETSEEAKGGAAPEGPNEAEVTSGKPEQEVPDAEEEKSVSGTDVQEECRE-KGGQEKQGEVIVSIEEK
          WLTE.SE.AKGG.APEGPNEAEVTSGKPEQEVPD.EEEKSVS.TDVQEECRE.KGG.EK..EVIVSIEEK
Retrocopy WLTEISEGAKGGGAPEGPNEAEVTSGKPEQEVPDVEEEKSVSETDVQEECRE<KGGWEKHREVIVSIEEK

Parental  PKEVSEEQPVVTLEKQGTAVEVEAESLDPTVKPVDVGGDEPEEKVVTSENEAGKAVLEQLVGQEVPPAEE
          PKEVSEEQ.VV.LEKQGTAVEV.AESLDPTVKPVDVGGDEPEEKVVTSE..AGK.VLE.LVGQEVPPAEE
Retrocopy PKEVSEEQTVVILEKQGTAVEVAAESLDPTVKPVDVGGDEPEEKVVTSE-KAGKVVLE*LVGQEVPPAEE

Parental  SPEVTTEAAEASAVEAGSEVSEKPGQEAPVLPKDGAVNGPSVVGDQTPIEPQTSIERLTETKDGSGLEEK
          SPEVTTEAAEASA.EAGSEVSEKPGQEA.VLPKDGAVNGPS.VGDQTP.EPQTSIERLTETKDGSGLEEK
Retrocopy SPEVTTEAAEASALEAGSEVSEKPGQEATVLPKDGAVNGPSAVGDQTPTEPQTSIERLTETKDGSGLEEK

Parental  VRAKLVPSQEETKLSVEESEAAGDGVDTKVAQGATEKSPEDKVQIAANEETQER-EEQMKEGEETEGSEE
          VRAKLVPSQEETKLSVEESEAAGDGVDTKVAQGATEKSPEDKVQIAANEET.ER..EQ.KEGEETEG.EE
Retrocopy VRAKLVPSQEETKLSVEESEAAGDGVDTKVAQGATEKSPEDKVQIAANEETKER>DEQIKEGEETEGLEE

Parental  DDKENDKTEEMPNDSVLENKSLQENEEEEIGNLELAWDMLDLAKIIFKRQETKEAQLYAAQAHLKLGEVS
          DDKENDK.EEMPNDSVLENKSLQENEEEEIGNLELAWD.LDLAKI.FKRQETK.AQLY.AQAHLKLGEV.
Retrocopy DDKENDKAEEMPNDSVLENKSLQENEEEEIGNLELAWDTLDLAKIVFKRQETK-AQLYVAQAHLKLGEVG

Parental  VESENYVQAVEEFQSCLNLQEQYLEAHDRLLAETHYQLGLAYGYNSQYDEAVAQFSKSIEVIENRMAVLN
          VESENYVQAVEEFQSCLNL.EQYLEA.D.LLAETHYQLGLAYGYN.QYDEAVAQFSKSIEVIE.RMAVLN
Retrocopy VESENYVQAVEEFQSCLNL*EQYLEAYDHLLAETHYQLGLAYGYNFQYDEAVAQFSKSIEVIEKRMAVLN

Parental  EQVKEAEGSSAEYKKEIEELKELLPEIREKIEDAKESQRSGNVAELALKATLVESSTSGFTPGGGGSSVS
          EQVKEAEGSSAEYKKEIEELKELLPEI.EK.EDAKESQ..GNVAELALKATLVESSTSGFTP.GGGSSVS
Retrocopy EQVKEAEGSSAEYKKEIEELKELLPEITEKTEDAKESQTTGNVAELALKATLVESSTSGFTPSGGGSSVS

Parental  -MIASRKPTDGASSSNCVTDISHLVRKKRKPEEESPRKDDAKKAKQEPEVNGGSGDAVPSGNEVSENMEE
          ..IASRKPTDGASSSNCVTDISH.VRKKRKPEE.SP.KDDAKK.KQE.EVNGGSGDAVPSGNEV.ENMEE
Retrocopy <LIASRKPTDGASSSNCVTDISHFVRKKRKPEEQSPWKDDAKKVKQELEVNGGSGDAVPSGNEVLENMEE

Parental  EAENQAESRAAVEGTVEAGATVESTAC
          EAEN..ESRAAVEGTVEAGAT.ESTAC
Retrocopy EAENRVESRAAVEGTVEAGATAESTAC

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	80.70 RPM
bodymap2_adrenal	0.98 RPM	118.15 RPM
bodymap2_brain	0.07 RPM	61.20 RPM
bodymap2_breast	0.00 RPM	52.02 RPM
bodymap2_colon	0.02 RPM	57.54 RPM
bodymap2_heart	0.00 RPM	38.57 RPM
bodymap2_kidney	0.00 RPM	52.18 RPM
bodymap2_liver	0.00 RPM	23.66 RPM
bodymap2_lung	0.00 RPM	64.50 RPM
bodymap2_lymph_node	0.02 RPM	83.05 RPM
bodymap2_ovary	0.02 RPM	100.43 RPM
bodymap2_prostate	0.00 RPM	61.43 RPM
bodymap2_skeletal_muscle	0.02 RPM	19.66 RPM
bodymap2_testis	0.02 RPM	207.63 RPM
bodymap2_thyroid	0.00 RPM	68.87 RPM
bodymap2_white_blood_cells	0.00 RPM	52.86 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4064 was not detected

EST

No EST(s) were mapped for retro_hsap_4064 retrocopy.

TSS

No TSS is located nearby retro_hsap_4064 retrocopy 5' end.

Lab

retro_hsap_4064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4064 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2754
Pongo abelii	retro_pabe_3338

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010436	1 retrocopy	retro_chof_2560,
Homo sapiens	ENSG00000132780	1 retrocopy	retro_hsap_4064 ,
Macropus eugenii	ENSMEUG00000001037	1 retrocopy	retro_meug_1359,
Mus musculus	ENSMUSG00000028693	1 retrocopy	retro_mmus_1217,
Nomascus leucogenys	ENSNLEG00000014434	1 retrocopy	retro_nleu_564,
Pongo abelii	ENSPPYG00000001409	1 retrocopy	retro_pabe_3338,
Pan troglodytes	ENSPTRG00000000677	1 retrocopy	retro_ptro_2754,