RetrogeneDB ID: retro_pabe_2217

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:56122999..56124589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARG2
• Ensembl ID: ENSPPYG00000006527
• Aliases: None
• Description: NMDA receptor regulated 2 [Source:HGNC Symbol;Acc:29885]

Sequence

>retro_pabe_2217
CAGAGAGAGCAGAGGAGTTATGTGGACTTGTTGGTTAAATATGCAAAGATTTCTGCAAATTCCAAAGCTATCGGAATAAA
GAAAAAATGACTTTTTGCCGTACTTGGATATGAAAAAAACATGTGAATGAAGAAGTTACTGAGTTCCTAAAGTTTTTGCA
GAATTCTGCAAAGAAATGTGCACAGGATTATAATATGCTTTCTGATGATGCTTGTCTCTTCACAGAGAAAATTTTAAGAG
CTTGCATTGAACAAGTGAAAAAGTTCCTAGAATTCTATACTCTCCACGAGGTCACCAGCTTAATGGTATTCTTCCCATTC
AGAGTAGAGATGGAATTAAAGTTAGAAAAAAAACTCTTCTTGCATTGGGCAGGGTGAAATATGTGAAAACAGTATTTCCC
TCAATGCTTATAAAGTTGCAGCTCTCAAAAGATGATATATCTACCATTGAATTGCCAGAATGAACAGCTGAAGCTATGCA
TTATTATATTAGAAAAGATCCAAATGCAGAGAAGCTTGTTTCAAGATATCACCCTCAGCTAGCTCTAACTAGTCAATCAT
TATTTACCTTATTAAATAATTTTGGACCAATATACAAGGAACCCTGGGAACTTTCAGTATTGATTCAAGTAATACCTGTC
GCAGGTTCAAAACCAGTTAAAGTAATAACTATTAATTTGCCACTTCCCCGAAATAAAATAACTATGAGAGAGAGAAAACA
AATCTTTCATGAAGTTCCATTAAAATGTATGATGCCCCAAAACACATTTGTTCCAGTATCTGCAGTCTTTATGGACAAAC
CTGAAGAGTTTATATCTGAAATGGACATGTCCCATGAATTCAATGAGTGCCGAAAAACTGAGACTCTTGAAAGCTTGTAT
CTGGATTTTGATGATGAGGTCACAGAACTTGAAACTTTTGGAGTAACCACCACCAAGGCATCAAAGTCACCAATTCCAGC
AAGTACTTCCACAGTACCCAACATGACAGATGCTCCTACAGCCCCCAAAGCAGTAACTACACCTGTGGCACCAAGTGCAC
CAGACATTTCTGCTAATTCTAGAAGTTTATCTCAGATTCTGATTGAACAATTGCAAAAGGAGAAACAACTGGTCACTGGT
ATGGATGGTGGCCCTGAAGAATGCAAAAATAAAGATGATCAGACTTTGAATCATGTGGTGATAAGGTATCAAATTCTGAC
AAGTCTTTGATGCAAGATAGTGACTTGAAAACATCTGATGACTTACAGTTAGAAAATTCTGAGGAAATTGAAACTTCTAA
TAAAAATGATATGACTATAGATATGGTACATGCTGATGGTGAAAGACCCAATGTTCTGGAAAACCTAGACAACTCAAAGG
AAAAGCCTGTTAGATCAGAAGCAGCTAAAACTGAAGATGCAGTTCTCTTCAGCAGTGGTACAGATGAGGAGTGTTTAATC
ATTGATAGAGAGTGTAAAAATAATAGTGATGGAAAGACAGATGTTGTGGGTTCTAACTTAAGTTCTAGATCAGCTAGTCC
AAATTCTTTCTCAGGACAGGCTTCTGTAGGAAACAAGACTACTATTGTTTGTAGGCCTGCAGAGTCATGT

Alignment

ORF - retro_pabe_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 57.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QREQRSYVDLLVKYAKIPANSKAVGINK-NDYLQYLDMKK-HVNEEVTEFLKFLQNSAKKCAQDYNMLSD
          QREQRSYVDLLVKYAKI.ANSKA.GI.K.ND.L.YLDMKK.HVNEEVTEFLKFLQNSAKKCAQDYNMLSD
Retrocopy QREQRSYVDLLVKYAKISANSKAIGIKK>NDFLPYLDMKK>HVNEEVTEFLKFLQNSAKKCAQDYNMLSD

Parental  DARLFTERILRACIEQVKKYSEFYTLHEVTSLMGFFPFRVEM-GLKLEKT-LLALGSVKYVKTVFPSMPI
          DA.LFTE.ILRACIEQVKK..EFYTLHEVTSLM.FFPFRVEM.G.K.....LLALG.VKYVKTVFPSM.I
Retrocopy DACLFTEKILRACIEQVKKFLEFYTLHEVTSLMVFFPFRVEM<GIKVXXXXLLALGRVKYVKTVFPSMLI

Parental  KLQLSKDDIATIETSEQTAEAMHYDISKDPNAEKLVSRYHPQIALTSQSLFTLLNNHGPTYKEQWEIPVC
          KLQLSKDDI.TIE..E.TAEAMHY.I.KDPNAEKLVSRYHPQ.ALTSQSLFTLLNN.GP.YKE.WE..V.
Retrocopy KLQLSKDDISTIELPE*TAEAMHYYIRKDPNAEKLVSRYHPQLALTSQSLFTLLNNFGPIYKEPWELSVL

Parental  IQVIPVAGSKPVKVIYINSPLPQKKMTMRERNQIFHEVPLKFMMSKNTSVPVSAVFMDKPEEFISEMDMS
          IQVIPVAGSKPVKVI.IN.PLP..K.TMRER.QIFHEVPLK.MM..NT.VPVSAVFMDKPEEFISEMDMS
Retrocopy IQVIPVAGSKPVKVITINLPLPRNKITMRERKQIFHEVPLKCMMPQNTFVPVSAVFMDKPEEFISEMDMS

Parental  CEVNECRKIESLENLYLDFDDDVTELETFGVTTTKASKSPSPASTSTVPNMTDARTAPKAGTTTVAPSAP
          .E.NECRK.E.LE.LYLDFDD.VTELETFGVTTTKASKSP.PASTSTVPNMTDA.TAPKA.TT.VAPSAP
Retrocopy HEFNECRKTETLESLYLDFDDEVTELETFGVTTTKASKSPIPASTSTVPNMTDAPTAPKAVTTPVAPSAP

Parental  DISAHSRSLSQILMEQLQKEKQLVTGMDGGPEECKNKDGQ-GFESC-EKVSNSEKPLIQHSDLKTSDALQ
          DISA.SRSLSQIL.EQLQKEKQLVTGMDGGPEECKNKD.Q..FESC..KVSNS.K.L.Q.SDLKTSD.LQ
Retrocopy DISANSRSLSQILIEQLQKEKQLVTGMDGGPEECKNKDDQ<DFESCGDKVSNSDKSLMQDSDLKTSDDLQ

Parental  LENSQEIETSNKNDMTIDMVHADGERPNVLENVDNSKEKTVGSEAAKTEDTVLCSSDTDEECLIIDTECK
          LENS.EIETSNKNDMTIDMVHADGERPNVLEN.DNSKEK.V.SEAAKTED.VL.SS.TDEECLIID.ECK
Retrocopy LENSEEIETSNKNDMTIDMVHADGERPNVLENLDNSKEKPVRSEAAKTEDAVLFSSGTDEECLIIDRECK

Parental  NNCDGKTAVVGSNLSSRPASPNSSSGQASVGNQTNTACSPEESC
          NN.DGKT.VVGSNLSSR.ASPNS.SGQASVGN.T...C.P.ESC
Retrocopy NNSDGKTDVVGSNLSSRSASPNSFSGQASVGNKTTIVCRPAESC

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	0.17 RPM	6.19 RPM
SRP007412_cerebellum	0.12 RPM	15.81 RPM
SRP007412_heart	0.24 RPM	13.28 RPM
SRP007412_kidney	0.13 RPM	13.13 RPM
SRP007412_liver	0.03 RPM	9.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2217 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2217 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2672
Pan troglodytes	retro_ptro_1801
Gorilla gorilla	retro_ggor_1865

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000128915	1 retrocopy	retro_hsap_2672,
Gorilla gorilla	ENSGGOG00000022206	1 retrocopy	retro_ggor_1865,
Pongo abelii	ENSPPYG00000006527	1 retrocopy	retro_pabe_2217 ,
Pan troglodytes	ENSPTRG00000007133	1 retrocopy	retro_ptro_1801,