RetrogeneDB ID: retro_pabe_3338

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:62961849..62963920(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NASP
• Ensembl ID: ENSPPYG00000001409
• Aliases: None
• Description: nuclear autoantigenic sperm protein (histone-binding) [Source:HGNC Symbol;Acc:7644]

Sequence

>retro_pabe_3338
AAAGTGGAGAGAATGGAGAACGGTGTGTTGGGAAACACCTTGGAAGGTGTGTATGTGGAAGAGGAAGAAGGAGAAAAAAC
AGAAGATGAATCTCTGGTAGAAAATAATGATAACATAGGTGAGGAAGCAAGGGAAGAGTTGAGAGAACAGGTTTATGACG
CCATGGGAGAAAAAGAAGAAGCCAAAAAAACAGAAGACAAGTCTTTGGCAAAGCCTGAAACTGAAAAAGAATAGGACAGT
GAAATGGAGAAGGGTGGAAGAGAAGATATGGATATAAGTGAATCTGCAGAGGAGCCACAGGAAAAAGTTGACTTGATTCT
AGATTGGTTAACTGAAACCTCTGAAGGGGCAAAAGGAGGAGCAGCACCAGAAGGACGGAATGAAGCTGAGGTCACTTCTG
GGAAGTCAGAACAGGAAGTACCAGATGCTGAGGAAGAAAAATCAGTTTCTGAAACTGATGTCCAAGAAGAGTGCAGAGAA
AAAGGAGATCGGGAGAAGCATGGAGAGGTAATTGTGAGCATAGAGGAGAAGCCAAAAGAAGTTTCAGAAGAGCAGCCTAT
GATGACTCTAGAAAAGCAGGGCACTGCAATGGAGGTAGAAGCAGAGTCTTTAGACCCAACAATCAAGCCAGTAGATGTGG
GTGAGGACGAGCCAGAAGAGAAGGTAGTTACCTCTGAAAATGAGGCAGGAAAGGTGGTTCTTGAGCAACTGGTAGGTCAA
GAAGTGCCACCTGCTGAAGAGTCACCAGAGGTGACAACAGAGGCTGCAGAGGCCTCAGCTGTAGAGGCTGGATCAGAAGT
CTCTGAAAAGCCTGGGCAGGAGGCTACAGTTCTCCCTAAGGATGGTGCAGTTAATGGACTGTCAGCTATAGGAGATCAGA
CTCCTACTGAACCACAGACTTCTATAGAAAGACTGACAGAAACAAAAGATGGCTCAGGACTAGAGGAGAAGGTCAGGGCA
AAGCTGGTTCCTAGTCAGGAGGAGACTAAGCTGTCTGTAGATGAGTCTGAGGCAGCTGGAGATGGGGTTGATACCAAGGT
AGCCCAGGGAGCTACTGAGAAATCACCTGAAGACAAAGTTCAGATAGCTGCTAATGAAGAGACAAAAGAGAGAGAAGAAC
AGATAAAAGAGGGTGAAGAAACTGAAGGCTCAGAAGAGGATGATAAAGAAAATGATAAGACTGAAGAAATGCCAAATGAT
TCAGTCCTTGAAAACAAGTCTCTTCAAGAAAATGAAGAGGAGGAAATTGGGAACCTAGAGCTTGCCTAGGATATGCTGGA
TTTAGCAAAGATCGTTTTTAAAAGGCAAGAAGCAAAAGCCCAGCTTTATGTTGCCCAGGCACATCTTAAACTCGGAGAAG
TTAGTGTTGAATCTGAAAACTATGTGCAAGCTGTGGAGGAGTTCCAGTCCTGCCTAAACCCATAGGAACAGTACCTGGAA
GCCCACGACCGTCTCCTTGCAGAGACCCACTACCAGCTGGGCTTGGCTTATGGGTACAACTCTCAGTATGATGAGGCAGT
GGCACAGTTCAGCAAATCTATTGAAGTCATTGAGAAGAGAATGGCTGTACTAATCGAGCAGGTGAAGGAGGCTGAAGAAT
CGTCTGCTGAATACAAGAAAGAAATCGAGGAACTGAAGGAACTGCTACCCGAAATTAGAGAGAAGACAGAAGATGCAAAG
GAGTCTCAGCGTACTGTGAATGTAGCTGAACTGGCTCTGAAAGCTACTCTGGTGGAGAGCTCTACTTCAGGTTTCACTCC
TAGTGGAGGAGGCTCTTCAGTCTCCATGATTGCCAGTAGAAAGCCAACAGATGGTGCTTCCTCATCAAATTGTGTGACTG
ATATTTCCCACCTTGTCAGAAAGAAGAGGAAACCAGAGGAACAGAGTCCCCGAAAGATGATGCAAAGAAAGCCAAACAAG
AGCGGGAGGTGAATGGAGGCAGTGGAGATGCTGCCCCCAGTGGAAATGAAGTTTCAGAAAACATGGAGGAGGAGGCTCAG
AATCGGGCTGAAAGCTGGGCGGCAGTGGAGGGGACAGTGGAGGCGGAGCTACAGTTGAAAGCACTGCATGT

Alignment

ORF - retro_pabe_3338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.35 %
• Parental protein coverage: 87.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELARMENGVLGNALEGVHVEEEEGEKTEDESLVENNDNIDEEAREELREQVYDAMGEKEEAKKTEDKSLA
          ...RMENGVLGN.LEGV.VEEEEGEKTEDESLVENNDNI.EEAREELREQVYDAMGEKEEAKKTEDKSLA
Retrocopy KVERMENGVLGNTLEGVYVEEEEGEKTEDESLVENNDNIGEEAREELREQVYDAMGEKEEAKKTEDKSLA

Parental  KPETDKEQDSEMEKGGREDMDISESAEEPQEKVDLTLDWLTETSEEANGGAAPEGPNEAEVTSGKPEQEV
          KPET.KE.DSEMEKGGREDMDISESAEEPQEKVDL.LDWLTETSE.A.GGAAPEG.NEAEVTSGK.EQEV
Retrocopy KPETEKE*DSEMEKGGREDMDISESAEEPQEKVDLILDWLTETSEGAKGGAAPEGRNEAEVTSGKSEQEV

Parental  PDAEEEKSVSGTDVQEEYREKGGQEKQGEVIVSIE-KPKEVSEEQPVVTLEKQGTAVEVEAESLDPTVKP
          PDAEEEKSVS.TDVQEE.REKG..EK.GEVIVSIE.KPKEVSEEQP..TLEKQGTA.EVEAESLDPT.KP
Retrocopy PDAEEEKSVSETDVQEECREKGDREKHGEVIVSIEEKPKEVSEEQPMMTLEKQGTAMEVEAESLDPTIKP

Parental  VDVGGDEPEEKVVTSENEAGKAVLEQLVGQEVPPAEESPEVTTEAAEASAVEAGSEVSEKPGQEAPVLPK
          VDVG.DEPEEKVVTSENEAGK.VLEQLVGQEVPPAEESPEVTTEAAEASAVEAGSEVSEKPGQEA.VLPK
Retrocopy VDVGEDEPEEKVVTSENEAGKVVLEQLVGQEVPPAEESPEVTTEAAEASAVEAGSEVSEKPGQEATVLPK

Parental  DGAVNGPSVVGDQTPIEPQTSIERLTETKDGSGLEEKVRAKLVPSQEETKLSVEESEAAGDGVDTKVAQG
          DGAVNG.S..GDQTP.EPQTSIERLTETKDGSGLEEKVRAKLVPSQEETKLSV.ESEAAGDGVDTKVAQG
Retrocopy DGAVNGLSAIGDQTPTEPQTSIERLTETKDGSGLEEKVRAKLVPSQEETKLSVDESEAAGDGVDTKVAQG

Parental  ATEKSPEDKVQIAANEETQEREEQMKEGEETEGSEEDDKENDKTEEMPNDSVLENKSLQENEEEEIGNLE
          ATEKSPEDKVQIAAN...............TEGSEEDDKENDKTEEMPNDSVLENKSLQENEEEEIGNLE
Retrocopy ATEKSPEDKVQIAANXXXXXXXXXXXXXXXTEGSEEDDKENDKTEEMPNDSVLENKSLQENEEEEIGNLE

Parental  LAWDMLDLAKIIFKRQETKEAQLYAAQAHLKLGEVSVESENYVQAVEEFQSCLNLQEQYLEAHDRLLAET
          LA.DMLDLAKI.FKRQE.K.AQLY.AQAHLKLGEVSVESENYVQAVEEFQSCLN..EQYLEAHDRLLAET
Retrocopy LA*DMLDLAKIVFKRQEAK-AQLYVAQAHLKLGEVSVESENYVQAVEEFQSCLNP*EQYLEAHDRLLAET

Parental  HYQLGLAYGYNSQYDEAVAQFSKSIEVIEKRMAVLNEQVKEAEGSSAEYKKEIEELKELLPEIREKIEDA
          HYQLGLAYGYNSQYDEAVAQFSKSIEVIEKRMAVL.EQVKEAE.SSAEYKKEIEELKELLPEIREK.EDA
Retrocopy HYQLGLAYGYNSQYDEAVAQFSKSIEVIEKRMAVLIEQVKEAEESSAEYKKEIEELKELLPEIREKTEDA

Parental  KESQHSGNVAELALKATLVESSTSGFTPGGGGSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEEES
          KESQ...NVAELALKATLVESSTSGFTP.GGGSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEE.S
Retrocopy KESQRTVNVAELALKATLVESSTSGFTPSGGGSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEEQS

Parental  PR-KDDAKKAKQEPEVNGGSGDAVPSGNEVSENMEEEAENRAESRAAVEGTVEA-GATVESTAC
          PR.KDDAKKAKQE.EVNGGSGDA.PSGNEVSENMEEEA.NRAES.AAVEGTVEA.GATVESTAC
Retrocopy PR<KDDAKKAKQEREVNGGSGDAAPSGNEVSENMEEEAQNRAESWAAVEGTVEA<GATVESTAC

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
SRP007412_brain_prefrontal_cortex	4.59 RPM	28.42 RPM
SRP007412_cerebellum	11.80 RPM	63.60 RPM
SRP007412_heart	2.26 RPM	16.38 RPM
SRP007412_kidney	5.34 RPM	27.61 RPM
SRP007412_liver	5.69 RPM	29.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3338 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3338 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4064
Pan troglodytes	retro_ptro_2754

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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,