RetrogeneDB ID: retro_ptro_1801

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:90580808..90583329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARG2
• Ensembl ID: ENSPTRG00000007133
• Aliases: None
• Description: None

Sequence

>retro_ptro_1801
CAGAGAGAGCAGAGGAGTTATGTGGACTTGTTGGTTAAATATACAAAGATTTCTGCAAATTCCAAAACTATCAGAATAAA
GAAAAAATGACTTCTTGTAGTACTTGGATATGAAAAAAACATGTGAATGAAGAAGTTACTGAGTTCCTAAAGTTTTTGCA
GAATTCTGCAAAGAAATGTGCACAGGATTATAATATGCTTTCTGATGATGCTTGTCTCTTCACAGTGAAAATTTTAAGAG
CTTGCATTGAACAACTGAAAAAGTTCCTAGAATTCTACACTCTCCACGAGGTCACCAGCTTAATGGTATTCTTCCCATTC
AGAGAAGAGATGGAATTAAAGTTAGAAAAATCTCTTCTTGCATTGGGCAGGGTAAAATATGTGAAAACAGTATTTCCCTC
AATGCTTATAAAGTTGCAGCTCTCAAAAGATGATATATTGCCATTGAATTGCCAGAATGAACGGCTGAAGCTATGCCTTA
TTATATTAGAAAAGATCCAAATGCAGAGAAGCTTATTTCAAGATATCACCCTCAGCTAGCTCTAACTAGTCAATCATTAT
TTACTTTATTAAATAATCATGGACCAACGTACAAGGAACCTTGGGGACTTTCAGTATTGATTCAAGTAATACCTGTTGCA
GGTTCAAAACCAGTTAAAAGTAATATATATTAATTGGCCACTTCCCCGAAATAAAATAACTATGAGAGAGGGAAAACAAA
TCTTTCATGAAGTTCCATTAAAATTTATGATGCCCCAAAACACATTTGTTCCAGTATCTGCAGTCTTTATGGACAAACCT
GAAGAGTTTATATCTGAAATGGACATGTCCCATGAATTCAATGAGTGCCGAAAAATTGAGACTCTTGAAAACTTGTATCT
GGATTTTGATGATGAGGTCACAGAACTTGAAACTTTTGGAGTAACCACCACCAAAGCATCAAAGTCACTAATTCCAGCAA
GTACTTCCACAGTACCTAACATGACAGATGCTCCTACAGCCCCCAAAGCAGTAACAACACCTGTGGCACCAAGTGCACCA
GACATTTCTGCTAATTCTAGAAGTTCATCTCAGATTCTGATTGAACAATGGCAAAGGAGAAACAACTTGTCACTGGTATG
GATGTTGGCCCTGAAGAGTGCAAAAATAAAGATGATCAGAGTTTGAATCATGTGGTGATAAGGTATCAAATTCTGACAAG
TCTTTGATGCAAGATAGTGACTTGAAAACATCTGATGCCTTACAGTTAGAAGATTCTTAGGAAATTGAAACTTCTAATAA
AAATGATATGACTATAGATATGGAACATGCTGATGGTGAAAGACCCAATGTTCTGGAAAACCTAGACAACTCAAAGGAAA
AGACTGTTAGATCAGAAGCAGCTAAAACTGAAGATACAGTTCTCTTCAGCAGTGATACAGATGAGGAGTGTTTAATCATT
GATAGAGAGTGTAAAAATAATAGCGATGGAAAGACAGATGTTGTGGGTTCTAACTTAAGTTTTAGATCAGCTAGTCCAAA
TTCTTCCTCAGGACAGGCTTCTGTAGGAAAACAGACTACTACTGTTTGTAGGCCTGCAGAGTCGTGTGTTTTTTTTAAAA
AACGTATCAAATGAGTATATAAAAAATATGATCCAGTTGGAGAAATTTTAAAAATGCAGGATGAGCTCTTAAAGCCAATT
TCCAGAAAAGTACCCAAACTGTCCTTAATGAATTTAGGAAATTCTAAACAGTCTTCTGTTTCTGAGCAATTGTCTGTTCC
TTCAGATGGCTCTAGTTGACCGAAATCTGGATGGCCTTCTGCATTTCAGAAGCCCAAAGGACAATTGCCATATGAACTTC
AGGACTATGTTGAAGATACATCAGAATACCTAGCTCCTCAGAAAGGAAATTTTGTTTATAAGTTATTTAGCCTTCAAGAT
CTGTTGTTTCTCATGTGCTGCAGTGTCCAGAGGATAGAGACAAGACCACATTCTAAAAGAACAGAAGAAAATCAGAAGAC
AATTTCCAGTTGATGTACTACCAAAAGTAGAGTATCAAGCTTGTTATGGAGTTGAAGCTCTGATTGAAAGTGAACTTTGT
CACTTAAGGACTGAAAGTTTATTAAATTCCAACAGCTCATTTTATGTTGGGCATATTGATGCATTTACTTCAAAGCATTT
TCTACTGGAAGAAACTACCTCAGAAGAATTAAAAGAAAAGCTTTCAGCACTCAAGATTTCCAATTTATTTAACATCCTCC
AACACAGTCTAAAGAAATTAAGTAGCTTGCAGGAGGGTTCCTACTTGTTATATCATGCAGCAGAAGATTCTTCACTCCTG
AACTATAAGGTCTCTGTTGGAAAAGTTACTAGGACAGCATACAATTTGTATAAAACCCATTGCAGCCTTCCTGGCGTACC
TTTCAGTCTCTCATTTCCCCGGGTTCCATTAGATCCCAGGCTGTTATTACCAAATCATATCCATCATGGAAGAATACCTT
GTACTTTTCCACCTAAATCACTGGATACCACAACAAAACGT

Alignment

ORF - retro_ptro_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.12 %
• Parental protein coverage: 85.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QREQRSYVDLLVKYAKIPANSKAVGINK-NDYLQYLDMKK-HVNEEVTEFLKFLQNSAKKCAQDYNMLSD
          QREQRSYVDLLVKY.KI.ANSK...I.K.ND.L.YLDMKK.HVNEEVTEFLKFLQNSAKKCAQDYNMLSD
Retrocopy QREQRSYVDLLVKYTKISANSKTIRIKK>NDFL*YLDMKK>HVNEEVTEFLKFLQNSAKKCAQDYNMLSD

Parental  DARLFTEKILRACIEQVKKYSEFYTLHEVTSLMGFFPFRVEMGLKLEKTLLALGSVKYVKTVFPSMPIKL
          DA.LFT.KILRACIEQ.KK..EFYTLHEVTSLM.FFPFR.EM.LKLEK.LLALG.VKYVKTVFPSM.IKL
Retrocopy DACLFTVKILRACIEQLKKFLEFYTLHEVTSLMVFFPFREEMELKLEKSLLALGRVKYVKTVFPSMLIKL

Parental  QLSKDDIT-TIETSEQTAEAMHYDISKDPNAEKLVSRYHPQIALTSQSLFTLLNNHGPTYKEQWEIPVCI
          QLSKDDI...IE..E.TAEAM.Y.I.KDPNAEKL.SRYHPQ.ALTSQSLFTLLNNHGPTYKE.W...V.I
Retrocopy QLSKDDIL<AIELPE*TAEAMPYYIRKDPNAEKLISRYHPQLALTSQSLFTLLNNHGPTYKEPWGLSVLI

Parental  QVIPVAGSKPVK-VIYINSPLPQKKMTMRERNQIFHEVPLKFMMSKNTSVPVSAVFMDKPEEFISEMDMS
          QVIPVAGSKPVK.VIYIN.PLP..K.TMRE..QIFHEVPLKFMM..NT.VPVSAVFMDKPEEFISEMDMS
Retrocopy QVIPVAGSKPVK>VIYINWPLPRNKITMREGKQIFHEVPLKFMMPQNTFVPVSAVFMDKPEEFISEMDMS

Parental  CEVNECRKIESLENLYLDFDDDVTELETFGVTTTKASKSPSPASTSTVPNMTDAPTAPKAGTTTVAASAP
          .E.NECRKIE.LENLYLDFDD.VTELETFGVTTTKASKS..PASTSTVPNMTDAPTAPKA.TT.VA.SAP
Retrocopy HEFNECRKIETLENLYLDFDDEVTELETFGVTTTKASKSLIPASTSTVPNMTDAPTAPKAVTTPVAPSAP

Parental  DISANSRSLSQILMEQLQ-KEKQLVTGMDGGPEECKNKDDQG-FESC-EKVSNSDKPLIQDSDLKISDAL
          DISANSRS.SQIL.EQ.Q.KEKQLVTGMD.GPEECKNKDDQ..FESC..KVSNSDK.L.QDSDLK.SDAL
Retrocopy DISANSRSSSQILIEQWQ<KEKQLVTGMDVGPEECKNKDDQS<FESCGDKVSNSDKSLMQDSDLKTSDAL

Parental  QLENSQEIETSNKNDMTIDMVHADGERPNVLENLDNSKEKTVGSEAAKTEDTVLCSSDTDEECLIIDTEC
          QLE.S.EIETSNKNDMTIDM.HADGERPNVLENLDNSKEKTV.SEAAKTEDTVL.SSDTDEECLIID.EC
Retrocopy QLEDS*EIETSNKNDMTIDMEHADGERPNVLENLDNSKEKTVRSEAAKTEDTVLFSSDTDEECLIIDREC

Parental  KNNSDGKTAVVGSNLSSRPASPNSSSGQASVGNQANTACSPEESCVL-KKPIKRVYKKFDPVGEILKMQD
          KNNSDGKT.VVGSNLS.R.ASPNSSSGQASVG.Q..T.C.P.ESC...KK.IK.VYKK.DPVGEILKMQD
Retrocopy KNNSDGKTDVVGSNLSFRSASPNSSSGQASVGKQTTTVCRPAESCXXXKKRIK*VYKKYDPVGEILKMQD

Parental  ELLKPISRKVPELPLMNLENSKQPSVSEQLSGPSDSSSWLKSGWPSAFQKPKGRLPYELQDYVEDTSEYL
          ELLKPISRKVP.L.LMNL.NSKQ.SVSEQLS.PSD.SS..KSGWPSAFQKPKG.LPYELQDYVEDTSEYL
Retrocopy ELLKPISRKVPKLSLMNLGNSKQSSVSEQLSVPSDGSS*PKSGWPSAFQKPKGQLPYELQDYVEDTSEYL

Parental  APQEGNFVYKLFSLQDLLLLVRCSVQRIETRPRSKK-RKKIRRQFPVYVLPKVEYQACYGVEALTESELC
          APQ.GNFVYKLFSLQDLL.L..CSVQRIETRP.SK...KKIRRQFPV.VLPKVEYQACYGVEAL.ESELC
Retrocopy APQKGNFVYKLFSLQDLLFLMCCSVQRIETRPHSKR>QKKIRRQFPVDVLPKVEYQACYGVEALIESELC

Parental  RLWTESLLHSNSSFYVGHIDAFTSKLFLLEEITSEELKEKLSALKISNLFNILQHILKKLSSLQEGSYLL
          .L.TESLL.SNSSFYVGHIDAFTSK.FLLEE.TSEELKEKLSALKISNLFNILQH.LKKLSSLQEGSYLL
Retrocopy HLRTESLLNSNSSFYVGHIDAFTSKHFLLEETTSEELKEKLSALKISNLFNILQHSLKKLSSLQEGSYLL

Parental  SHAAEDSSLLIYKASDGKVTRTAYNLYKTHCGLPGVPSSLSVPWVPLDPSLLLPYHIHHGRIPCTFPPKS
          .HAAEDSSLL.YK.S.GKVTRTAYNLYKTHC.LPGVP.SLS.P.VPLDP.LLLP.HIHHGRIPCTFPPKS
Retrocopy YHAAEDSSLLNYKVSVGKVTRTAYNLYKTHCSLPGVPFSLSFPRVPLDPRLLLPNHIHHGRIPCTFPPKS

Parental  LDTTTQQ
          LDTTT..
Retrocopy LDTTTKR

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	0.00 RPM	12.46 RPM
SRP007412_cerebellum	0.00 RPM	15.85 RPM
SRP007412_heart	0.00 RPM	21.60 RPM
SRP007412_kidney	0.00 RPM	28.40 RPM
SRP007412_liver	0.03 RPM	12.54 RPM
SRP007412_testis	1.90 RPM	26.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1801 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1801 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2672
Gorilla gorilla	retro_ggor_1865
Pongo abelii	retro_pabe_2217

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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 ,