RetrogeneDB ID: retro_nleu_1292

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397287.1:27166789..27169560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDLBP
• Ensembl ID: ENSNLEG00000013818
• Aliases: None
• Description: None

Sequence

>retro_nleu_1292
ATGAGTTCTGTTGCAGTTTTGACCCAAGAGAGTTTTGCTGAACACCGAAGTGGGCTGGTTCCGCAACAAATCAAAGTTGC
CATTCTAAATTCAGAAGAGGAGAGCAACCCTCCAACCTACAAAGATGCCTTCCCTCCACTTCCTGAGAAAGCTGCTTGCC
TGGAAAGTGCCCAGGAACATGCTGCAGCCTGGGGGAACAAGATCCGGCCCATCAAGGCTTCTGTCATCACTCAGGTCCAT
GTGCCCCTGGAGGAGAGAAAATATACGGATATGAACCAATTTGGAGAAGGTGAACAAGCAAAAATCTGCCTTGAGATCAT
GCAGAGAACGGGTGCTCACTTGGAGCTGTCTTTGGCCAAAGACCAAGGCCTCTCCATCATGGTGTCAGGAAAGCTGGATG
CTGTCATGAAAGCTTGGAAGGACATTGTTGGTAGACTGCAGACTCAGGCCTCAGCAACTGTTGCCATTCCCAAAGAACAC
CGTCACTTTGTTATTGGCAAAAATGGAGAGAAACTACAAGACTTGGAGCTAAAAACTGCAACCAAAATCCAGATCCCATG
CCCAGATGACCCCAGCAATCAGATCAAGATCACCGGCACCAAAGAGGGTATCAAGAAAGCTCGCCATGAAGTCTTGCTCA
TCTCTGCTGAGCAGGACAAACATGCTGTGGAAAGGCTAGAAGTAGAAAAGGTGTTCCACCCCTTCATCACTGGGCCATAT
AACAGACTGGTTGGCGAGATCATGCAAGAGACAGGCACGCATATCAACATCCCCCCATCCAGCATGAACCGGACAGAGAT
TGTCTTCACTGGAGAGAAGGTACAATTGGCTCAGGCTGTGGCTCATCAAGATTTTGAGGAGAAGAAAAAGACTACAACCA
TCGCAGTGGAAGTGAAGAAATCCCAACGTAAGTATGTCATCGGGCCCAAGGGCAATTCACTGCAGGAGATCCTTGAGAGA
AGTGGAGTTTCCGTTGAGATCCCGCCCTCAGACAGCATCTCTGAGACTGTAATACTTCAAGGCGAACCTGAAAAGTTAGG
TCAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGCTTCACCGTCTCCTCGGTCACTGCCCCTTCCTGGCTTCACCGTT
TCATCATTGGCAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAGATGCCAAAGGTTCACATCGAGTTCACAGAGGGC
GAAGACAAGATCACCCTGGAGGGCCCTATAGAGGATGTCAATGTGGCCCAGGAACAGATAGAACGCATGGTCAAAGATTT
GATTAACCGGATGGACTACGTGGAGATCAACATCGACCACAAGTTCCACAGGCACCTCACTGGGAAGAGCAGCACCAACA
TAAACAGAATCAAAGGCCAGTACAAGGTGTCCGTGCACATCCCTCCTGACAGTAAGAAAAGCAATTTGATCCGCATCGTG
GGGGACACACAGGTGTGCAGCAGGCCAAGCGAGAGCTGCTGGAGCTTGCATCTCGCATGGAAAACGAGCATACCAAGGAT
CCAATCATTGAGCAAAGATTTCATCACACAATCGTTGGGCAGAAGGGTGAATGGATCCATGAAATTCGTGACAAATTCCC
AGAGGTCATCATCAACTTTCCAGACCCAGCACAAAAAAGTGACATTGTCCAGCTCAGAGGACCCAAGAATGCGGTGGAAA
AATGCACAAAATGCATGCAGAAGATGGTGGCAGATCTGGTGGAAAATAGCTATTCAATTTATGTTCCGATCTTCAAACAG
TTTCACAAGAATATCATTGGGAAAGGAGGTGCAAACATTAAAAAGATTCATGAAGAAAGCAACACCAAGATCGACCATCC
AGCAGAAAATAGCAATTCAGAGACCACTGTCATCACAGGCAAGTGAGCCAACTGCGAAGCTGCCCAGAGCAGGATTCTGT
CTATTCAGAAAGACCTGGCCAACATAGCCGAGGTAGAGGTCTCCATCCCTGCCAAGCTGCACAACTCCCTCATTGGCACC
AAGGGCCATCTGATCCGCTCCATCATGGAGGCGTGCGGTGGGGTCCACATTCACTTTCCCGTGGAAGGTTCAGGAAGCGA
CACCGTTGTTATCAGGGGCCCTTCCTTGGATGTGGAGAAGGCCAAGAAGCAGCTCCTGCATCTGTTGGAGGAGAAGCAAA
CCAAGAGTTTCACTGTTGACATCCGCGCCAAGCCAGAATATCACAAATTCCTCATGGGCAAGGGGGGCAGCAAAATTCGC
AAGGTCCGCGACAGCACTGGAGCACACGTCATCTTCCCTGCGGCTGAGGACAAGGACCAGGACCTAATCACCATCATCAG
ATAGGAGGATGCTGTCTGAGAGGCACAGAAGGAGCTGGAGGCCTTGATCCAAAACCTGGATAATGTGGTGGAAGACTCCA
TGCTGGTGGACCCCAAGCATCACTGCCACTTCGTCATCTGAAGAGGCCAGGTCTTGCAGGAGATTGCTGAAGAGTATGGC
GGAGTGATGGTCAGCTTCCCATGCTCTGGCACACAGAGCGACAAAGTCACCCTCAAGGGTGCCAAGGACTGTGTGGAGGC
AGCCAAGAAACGCATTCAGGAGACCACTGAGGAACTGGAAGCTCAGGTGTCATTAGAATGTGCTATACCCCAGAAATTCC
ACCTATCTGTCATGGGCCCCAAAGGTTCCAAAATCCAGCAGATTACTCGGGATTTCGACATTCAAATTAAATTCCCAGAC
AGAGAAGAGAACCCAGTTCATAGCGCAGAGCCAGTTGTCCAGGAAAATGGA

Alignment

ORF - retro_nleu_1292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.64 %
• Parental protein coverage: 73.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSVAVLTQESFAEHRSGLVPQQIKVATLNSEEESDPPTYKDAFPPLPEKAACLESAQEPAGAWGNKIRP
          MSSVAVLTQESFAEHRSGLVPQQIKVA.LNSEEES.PPTYKDAFPPLPEKAACLESAQE.A.AWGNKIRP
Retrocopy MSSVAVLTQESFAEHRSGLVPQQIKVAILNSEEESNPPTYKDAFPPLPEKAACLESAQEHAAAWGNKIRP

Parental  IKASVITQVFHVPLEERKYKDMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKAR
          IKASVITQV.HVPLEERKY.DMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKA.
Retrocopy IKASVITQV-HVPLEERKYTDMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKAW

Parental  KDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARH
          KDIV.RLQTQASATVAIPKEH..FVIGKNGEKLQDLELKTATKIQIP.PDDPSNQIKITGTKEGI.KARH
Retrocopy KDIVGRLQTQASATVAIPKEHRHFVIGKNGEKLQDLELKTATKIQIPCPDDPSNQIKITGTKEGIKKARH

Parental  EVLLISAEQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVNRTEIVFTGEKEQLAQA
          EVLLISAEQDK.AVERLEVEK.FHPFI.GPYNRLVGEIMQETGT.INIPP.S.NRTEIVFTG..E....A
Retrocopy EVLLISAEQDKHAVERLEVEKVFHPFITGPYNRLVGEIMQETGTHINIPPSSMNRTEIVFTG--EKVQLA

Parental  VARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKL
          .A......EEKKK.TTTIAVEVKKSQ.KYVIGPKGNSLQEILER.GVSVEIPPSDSISETVIL.GEPEKL
Retrocopy QAVAHQDFEEKKK-TTTIAVEVKKSQRKYVIGPKGNSLQEILERSGVSVEIPPSDSISETVILQGEPEKL

Parental  GQALTEVYAKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDRITLEGPTEDVNVA
          GQALTEVYAKANSFTVSSV.APSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGED.ITLEGP.EDVNVA
Retrocopy GQALTEVYAKANSFTVSSVTAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPIEDVNVA

Parental  QEQIEGMVKDLINRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQ-G
          QEQIE.MVKDLINRMDYVEINIDHKFHRHL.GKS..NINRIK.QYKVSV.IPPDS.KSNLIRI.GD.Q.G
Retrocopy QEQIERMVKDLINRMDYVEINIDHKFHRHLTGKSSTNINRIKGQYKVSVHIPPDSKKSNLIRIVGDTQ<G

Parental  VQQAKRELLELASRMENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRGP
          VQQAKRELLELASRMENE.TKD.IIEQRFH.TI.GQKGE.I.EIRDKFPEVIINFPDPAQKSDIVQLRGP
Retrocopy VQQAKRELLELASRMENEHTKDPIIEQRFHHTIVGQKGEWIHEIRDKFPEVIINFPDPAQKSDIVQLRGP

Parental  KNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETIII
          KN.VEKCTK.MQKMVADLVENSYSI.VPIFKQFHKNIIGKGGANIKKI.EESNTKID.PAENSNSET..I
Retrocopy KNAVEKCTKCMQKMVADLVENSYSIYVPIFKQFHKNIIGKGGANIKKIHEESNTKIDHPAENSNSETTVI

Parental  TGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDT
          TGK.ANCEAA.SRILSIQKDLANIAEVEVSIPAKLHNSLIGTKG.LIRSIME.CGGVHIHFPVEGSGSDT
Retrocopy TGK*ANCEAAQSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGHLIRSIMEACGGVHIHFPVEGSGSDT

Parental  VVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARVIFPAAEDK
          VVIRGPS.DVEKAKKQLLHL.EEKQTKSFTVDIRAKPEYHKFL.GKGG.KIRKVRDSTGA.VIFPAAEDK
Retrocopy VVIRGPSLDVEKAKKQLLHLLEEKQTKSFTVDIRAKPEYHKFLMGKGGSKIRKVRDSTGAHVIFPAAEDK

Parental  DQDLITIIGKEDAVREAQKELEALIQNLDNVVEDSMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPR
          DQDLITII..EDAV.EAQKELEALIQNLDNVVEDSMLVDPKHH.HFVI.RGQVL.EIAEEYGGVMVSFP.
Retrocopy DQDLITIIR*EDAV*EAQKELEALIQNLDNVVEDSMLVDPKHHCHFVI*RGQVLQEIAEEYGGVMVSFPC

Parental  SGTQSDRVTLKGAKDCVEAAKKRIQEIIEDLEAQVTLECAIPQKFHRSVMGPKGSRIQQITRDFSVQIKF
          SGTQSD.VTLKGAKDCVEAAKKRIQE..E.LEAQV.LECAIPQKFH.SVMGPKGS.IQQITRDF..QIKF
Retrocopy SGTQSDKVTLKGAKDCVEAAKKRIQETTEELEAQVSLECAIPQKFHLSVMGPKGSKIQQITRDFDIQIKF

Parental  PDREENPVHSTEPVVQENG
          PDREENPVHS.EPVVQENG
Retrocopy PDREENPVHSAEPVVQENG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1292 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,