RetrogeneDB ID: retro_pabe_1544

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:8231902..8235559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDLBP
• Ensembl ID: ENSPPYG00000013351
• Aliases: None
• Description: vigilin [Source:RefSeq peptide;Acc:NP_001127439]

Sequence

>retro_pabe_1544
ATGAGTTCTGTTGCAGTTTTGACCCAAGAGAGTTTTGCTGAACACCAAAGTGCGTTGGTTCCGCAACAAATCGAAGTTGC
CACTCTAAATTCAGAAGAGGAGAGCGACCCTCCAACCTATAAGGATGCCTTCCCTCCACTTCCTGAGAAAGCTGCTTGCC
TGGAAAGTACCCAGGAACCCGCTGGAGCCTGGGGGAACAAGATCCAGCCCATCACGGCTTCTGTCATCACTCAGGTCCAT
GTACCCCTGGAGGAGAGAAAATATAAGGCTATGAACCAATTTGGAGAAGGTGAACAAGCAAAAATCTGTCTTGAGATCAT
GCAGAGAACCGGTGCTCACTTGGAGCTGTCTTTGGCCAAAGACCAAGGCCTCTCCATCATGGTGTCAGGAAAGCTGGATG
CTGTCATGAAAGCTCGGAAGGACATTGTTGCGAGACTGCAGACTCAGGCCTCGGCAACTGTTGTCATTCCCAAAGAACAC
CATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTGGAGCTAAAAACTGCAACCAAAATCCAGATCCCATG
CCCAGATGACCCCAGCAATCAGATCAAGATCACTGGCACCAAAGAGAGCATCAAGAAAGCTCGCCATGAAGTCTTACTCA
TCTCTGCCAAGCAGGACAAACATGCTGTGGAGAGACTAGAAGTAGAAAAGGCATTCCACCCCTTCATCACTGGGCCATAT
AATAGACTGGTTGGTGAGATCATGCAAGAGACAGGCACATGCATCAACATCCCCCCACCCAGCATGAACCGGACAGAGAT
TGTCTTCACTGGAGAGAAGGAACAATTGGCTTAGGCTGTGGCTCGCATCAGGAAGATTTATGAGGAGAAGAAAAAGAAGA
CTACAACCATCGCAGTGGAAGTGAAGAAATCCCAACACAAGTATGTCATCGGGCCCAAGGGCAATTCATTGCAGGAGATC
CTTGAGAGAACTGGGGTTTCCATTGAGATCCCACCCTCAGACAGCATCTCTGAGACTGTAATACTTGGAGGCAAACCTGA
AAAGTTAGGTCAGGCGTTGACTGAAGTCTATGCCAAGGCCAATAGCTTCACCGTCTCCTCTGTCACCACCCCCTTCCTGG
CTTCACCGTTTCATCATTGGCAAGAAAGGGCAGAACGTGGCCAAAATCACTCAGCAGATGCCAAAGGTTCACATCAAGTC
ACAGAGGGTGAAGACAAGATCACCCTGGAGGGCCCTTAGAGGATGTCAGTGTGGCCCAGGAACAGATAGAAGGCATGGTC
AAAGATTTGATTAACCGGATGGACTATGTGGAGATCAACATCGACCACAATTTCCACAGGCACCTCATTGGGGAAGAGTG
GCGCCAACATAAACAGAATCAAAGGCCAGTACAAGGTGTCCGTGCGCACCCCCCTCCTGACAGTGAGAAGAGCAATCTGA
TCCACATTGAGGGGGACCCACGGGGTGTGCAGCAGGCCAACCGAGAGCTGATGGAGCTTGCATCTCACATGGAAAACGAG
CATACCAAGGATCTAATCATTGAGCAAAGATTTCATCACACAATCATTGGGCAGAAGGGTGAATGGATCCGTGAAATTCA
TGACAAATTCCCAGAGGTCATCATCAACTTTCCAGACCCAGCACAAAAAAGTGACATTGTCCAGCTCGGAGGACCCAAGA
ATGAAGTGGAAAAATGCACAAAATACATGCAGAAGATGGTGGCAGATCTGGTGGAAAATAGCTATTCAATTTCTGTTCCA
ATCTTCAAACAGTTTCACAAGAATATCATTGGGAAAGGAGGTGCAGACATTAAAAAGATTCGTGAAGAAAGCAACACCAA
GATCGACCTTCCAGGAGAGAACAGCAATTCAGAGACCATTGTCATCACAGGTGAGTGAGCCAACTGCGAAGCTGCCCGTA
GCAGGATTCTGTCTATTCAGAAAGACCTGGCCAACATAGCCGAGGTAGAGGTCTCCATCACTGCCAAGCTGCACAGCTCC
CTCATTGGCACCAAGGGCCGTCTGATCTGCTCCATCATGGATGAGTGCAGCAGGGTCCACATTCACTTTCCCATGGAAGG
TTCAGGAAGCAACACCATTGTTATCAGGGGCCCTTCCTCGGATGTGGAGAAGGCTAAGAAGCAGCTCCTGCATCTGGTGG
AGGAGAAGCAAACCAAGAGTTTCACTGTTGACATCCGCGCCAAGCCAGAATACCACAAATTCCTCATCAGCAAGGGTGGT
GGCAAAATTCGCAAGGTGCGCAACAGCACTGGAGCACATGTCATCTTCCCTGCGGCTGAAGACAAGGACCAGGACCTAAT
CACCATCACTGGAAAGGAGGACATTGTCTGAGAGGCACAGAAAGAGCTGGAGGCCTTGATCCAAAACCTGGATAATGTGG
TGGAAGACTCCATGCTGGTGGACCCCAAGCACCACTGCCACTTCGTCATCCGAAGAAGCCAGGTCTTGCGGGAGATTGCT
GAAGAGTATGGTGGGGTGATGGTCAGCTTCCCACACTCTGGCACACAGAGCGACAAAGTCATCCTCAAGGGTGCCAAGGA
CTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAGATCATTGAGGACCTGGAAGCTCAGGTGACATTAGAATGTGCTATAC
CCCTGAAATTCCATCGATCTGTCATGGGCCCCAAAGGTTCCAGAATCCAGCAGATTACTCAGGATTTCAATGTTCAAATT
AAATTCCCAGACAGAGAGGAAAACCCAGTTCACAGTAAAGAGCCAGTTGTCCAGGAAAATGGGGATGAAGCTGGGAAGGG
GAGAGAGGCTAAAGATTCTGACCCTGGCTCTCCAAGGAGGTGTGACATTATCATCATCTCCTGCTGGAAAGAAAAGTGTG
AGGCTGCCAAGGAAGCCCTGGAGGCATTGGTTCCTTCACCATGGAAGTAGAGGTGCCCTTTGACCTTCACCGTTACGTTA
CTGGGTGGAAGGGAAGTGGGATCTGCAAGATGATGGATGAGTTTGAGGTGAACGTACATGTCCCAGCACCTGAGCTACTG
TCTGACATCATTGCCATAACGGGCCTCACTGCAAATTTGGACTGGGCCAAGGCTGGACTGCTGGAGCATGTGAAGGAGCT
ACAGGCTGAGCAGGAGGACTGGGCTTTAAGGAGTTTTAAGCTGAGTGTCAATGTAGACCCCAAATACCATCCCAAGATTA
TTGGGAGAAAGGGGGCAGTAATTACCCAAATCTGGCTGGAGCATGATGTGAACATCTAGTTTCCTGATAAGGACGATGGG
AACCAGGACCAAATTACCATCACAGGGTACTAAAAGAACACAGAAGCTGCCAGAGATGCCATATTAAGAATTGTGGCTGA
ACTTGAGCAGAAGGTTTCTGAGGACGTCCCGCTGGACCACCGCGTTCATGCCTGCATCATCAGTGCTGTGGCAAAGCCAT
TTGCAAAATCATGGACGAATTCAAGGTGGGCATTCGCTTCCCACAGAGCGGAGCCCCAGACCCCAACTGCGTCACTGTGA
TGGGGCTCCCAGAGAATGTGGAGGAAGCCATCGACCACATCCTCAACTGGGAGAAGGAATACCTGGCTGACATGGTGGAC
AGTGAGGCGCTGCAGGTATACATGAAACCCCCGGCACACGAGGAGGCCAAGGCACCT

Alignment

ORF - retro_pabe_1544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.49 %
• Parental protein coverage: 96.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSSVAVLTQESFAEHRSGLVPQQIKVATLNSEEESDPPTYKDAFPPLPEKAACLESAQEPAGAWGNKIRP
          MSSVAVLTQESFAEH.S.LVPQQI.VATLNSEEESDPPTYKDAFPPLPEKAACLES.QEPAGAWGNKI.P
Retrocopy MSSVAVLTQESFAEHQSALVPQQIEVATLNSEEESDPPTYKDAFPPLPEKAACLESTQEPAGAWGNKIQP

Parental  IKASVITQVFHVPLEERKYKDMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKAR
          I.ASVITQV.HVPLEERKYK.MNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKAR
Retrocopy ITASVITQV-HVPLEERKYKAMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKAR

Parental  KDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARH
          KDIVARLQTQASATV.IPKEHHRFVIGKNGEKLQDLELKTATKIQIP.PDDPSNQIKITGTKE.I.KARH
Retrocopy KDIVARLQTQASATVVIPKEHHRFVIGKNGEKLQDLELKTATKIQIPCPDDPSNQIKITGTKESIKKARH

Parental  EVLLISAEQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVNRTEIVFTGEKEQLAQA
          EVLLISA.QDK.AVERLEVEKAFHPFI.GPYNRLVGEIMQETGT.INIPPPS.NRTEIVFTGEKEQLA.A
Retrocopy EVLLISAKQDKHAVERLEVEKAFHPFITGPYNRLVGEIMQETGTCINIPPPSMNRTEIVFTGEKEQLA*A

Parental  VARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKL
          VARI.KIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVS.EIPPSDSISETVIL.G.PEKL
Retrocopy VARIRKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSIEIPPSDSISETVILGGKPEKL

Parental  GQALTEVYAKANSFTVSSVAA-PSWLHRFIIGKKGQNLAKITQQMPKVHI-EFTEGEDKITLE-GPTEDV
          GQALTEVYAKANSFTVSSV...PSWLHRFIIGKKGQN.AKITQQMPKVHI...TEGEDKITLE.GP.EDV
Retrocopy GQALTEVYAKANSFTVSSVTT>PSWLHRFIIGKKGQNVAKITQQMPKVHI<QVTEGEDKITLE<GPLEDV

Parental  SVAQEHIEGMVKDLINRMDYVEINIDHKFHRHLI-GKSGANINRIKDQYKVSVRI-PPDSEKSN-LIRIE
          SVAQE.IEGMVKDLINRMDYVEINIDH.FHRHLI.GKSGANINRIK.QYKVSVR..PP.......LI.IE
Retrocopy SVAQEQIEGMVKDLINRMDYVEINIDHNFHRHLI>GKSGANINRIKGQYKVSVRT<PPPDSEKSNLIHIE

Parental  GDPQGVQQAKRELLELASRMENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIV
          GDP.GVQQA.REL.ELAS.MENE.TKDLIIEQRFH.TIIGQKGE.IREI.DKFPEVIINFPDPAQKSDIV
Retrocopy GDPRGVQQANRELMELASHMENEHTKDLIIEQRFHHTIIGQKGEWIREIHDKFPEVIINFPDPAQKSDIV

Parental  QLRGPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNS
          QL.GPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGA.IKKIREESNTKIDLP.ENSNS
Retrocopy QLGGPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGADIKKIREESNTKIDLPGENSNS

Parental  ETIIITGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG
          ETI.ITG..ANCEAARSRILSIQKDLANIAEVEVSI.AKLH.SLIGTKGRLI.SIM.EC..VHIHFP.EG
Retrocopy ETIVITGE*ANCEAARSRILSIQKDLANIAEVEVSITAKLHSSLIGTKGRLICSIMDECSRVHIHFPMEG

Parental  SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARVIFP
          SGS.T.VIRGPSSDVEKAKKQLLHL.EEKQTKSFTVDIRAKPEYHKFLI.KGGGKIRKVR.STGA.VIFP
Retrocopy SGSNTIVIRGPSSDVEKAKKQLLHLVEEKQTKSFTVDIRAKPEYHKFLISKGGGKIRKVRNSTGAHVIFP

Parental  AAEDKDQDLITIIGKEDAVREAQKELEALIQNLDNVVEDSMLVDPKHHRHFVIRRGQVLREIAEEYGGVM
          AAEDKDQDLITI.GKED.V.EAQKELEALIQNLDNVVEDSMLVDPKHH.HFVIRR.QVLREIAEEYGGVM
Retrocopy AAEDKDQDLITITGKEDIV*EAQKELEALIQNLDNVVEDSMLVDPKHHCHFVIRRSQVLREIAEEYGGVM

Parental  VSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTLECAIPQKFHRSVMGPKGSRIQQITRDFS
          VSFP.SGTQSDKV.LKGAKDCVEAAKKRIQEIIEDLEAQVTLECAIP.KFHRSVMGPKGSRIQQIT.DF.
Retrocopy VSFPHSGTQSDKVILKGAKDCVEAAKKRIQEIIEDLEAQVTLECAIPLKFHRSVMGPKGSRIQQITQDFN

Parental  VQIKFPDREENPVHSTEPVVQENGDEAGEGREAKDSDPGSPRRCDIIIISGRKEKCEAAKEALEALVP-V
          VQIKFPDREENPVHS.EPVVQENGDEAG.GREAKDSDPGSPRRCDIIIIS..KEKCEAAKEALEALVP..
Retrocopy VQIKFPDREENPVHSKEPVVQENGDEAGKGREAKDSDPGSPRRCDIIIISCWKEKCEAAKEALEALVP<F

Parental  TVEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQA
          T.EVEVPFDLHRYV.G.KGSGI.KMMDEFEVN.HVPAPEL.SDIIAITGL.ANLD.AKAGLLE.VKELQA
Retrocopy TMEVEVPFDLHRYVTGWKGSGICKMMDEFEVNVHVPAPELLSDIIAITGLTANLDWAKAGLLEHVKELQA

Parental  EQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA
          EQED.ALRSFKLSV.VDPKYHPKIIGRKGAVITQI.LEHDVNI.FPDKDDGN..QDQITITGY.KNTEAA
Retrocopy EQEDWALRSFKLSVNVDPKYHPKIIGRKGAVITQIWLEHDVNI*FPDKDDGN--QDQITITGY*KNTEAA

Parental  RDAILRIVGELEQMVSEDVPLDHRVHARIIGA-RGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN
          RDAILRIV.ELEQ.VSEDVPLDHRVHA.II.A..GKAI.KIMDEFKV.IRFPQSGAPDPNCVTV.GLPEN
Retrocopy RDAILRIVAELEQKVSEDVPLDHRVHACIISA<CGKAICKIMDEFKVGIRFPQSGAPDPNCVTVMGLPEN

Parental  VEEAIDHILNLEEEYLADVVDSEALQVYMKPPVHEEAKAP
          VEEAIDHILN.E.EYLAD.VDSEALQVYMKPP.HEEAKAP
Retrocopy VEEAIDHILNWEKEYLADMVDSEALQVYMKPPAHEEAKAP

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	0.44 RPM	227.85 RPM
SRP007412_cerebellum	0.36 RPM	116.74 RPM
SRP007412_heart	0.42 RPM	183.51 RPM
SRP007412_kidney	0.10 RPM	311.38 RPM
SRP007412_liver	0.18 RPM	334.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1544 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1544 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012829	1 retrocopy	retro_ecab_1042,
Loxodonta africana	ENSLAFG00000014826	1 retrocopy	retro_lafr_1146,
Mus musculus	ENSMUSG00000034088	1 retrocopy	retro_mmus_194,
Nomascus leucogenys	ENSNLEG00000013818	1 retrocopy	retro_nleu_1292,
Pongo abelii	ENSPPYG00000013351	1 retrocopy	retro_pabe_1544 ,