RetrogeneDB ID: retro_nleu_558

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:5682653..5684379(-)
• Located in intron of: ENSNLEG00000001093

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000026690
• Aliases: None
• Description: None

Sequence

>retro_nleu_558
GACCACGCGGAGGTGTTCAGGAACAGCTTCTGCCTCATCTATGCCATCCACGTGGAGGGCCTGAATGTGTTCCCGGGGAA
CGTAATTGGGAACCTGCCGACGTGCACCGTGCCCCTGGCTGGGGGCTCAAAGAGGATGATCTCTTTGGGGGCTGGTGACC
GCAGGTCATCCACACTCCACTGGCCGACTCGCTGTCCATCAGCAGCTGCAGCGTGGCCCTGCTCTTCTGCCAGCTGGGCA
TCATCAACATGCTGTCTTTGTTCTGTGCCGCCCTCACGGAGCACAAGGTTCTCTTCCAGTCCCAGAGCTACCAGCAGCTA
GCTAATGCCTGCAGGGGCCTCCTGGCATTGCTGTTTCCTGTCAGATACAGCTTCACCTATGGGCCCATCCTGCCGGCCCA
GCTGCTGGAGGCCCTCAGCACACCCACGCCCTTCATTATCGGGGTCAACGCGGCCTTCCAGGCAGAGACCCAGGAGCTGC
TAGACGTGATTGTTGCTGATCTAGATGGAGGGACGGTGACCATCCCTGAGTGTGTGCACATTCCACCCTCGCTAGAGCCA
CTGCAGAGTCAGACGCACAGTGTTCTGGGTACGGTCCTGGACCCGGAGCTGGAGTTGGTTAACCTCGCCTTCCCTCCACC
CACGACGTCCCCCTCCTCCCTGAAGATGCAGGACAAAGAGCTGGGTGCCCTCTTCCTGTGGCTCTTCGATCAGCTGCTGC
AGGGCTATCTCTGGTGCCTGCACGTCGTGCGCATTCACCCAGAGCCTGTCATCCGCTTCCATAAAGCAGCCTTCCTGGCC
CAGTGTGGGCTGGTGGAGGACGATTTCCTGATGAAGGTGCTGGAGGGCGTGGCCTTTGCTCTCTTCGTGTCGGAGCATGG
GTTCCTGTACCTCCACACAGACCTGTTTGATGAGCTGGTGGTCCACGAGGTGGCACGGAGGTGGGTGGATGAGAAACATG
TCTTGCCTCACATCCAGGAACTGGCAGTGCAGGTCTACAAGAATGAGAACCTGTACCCAGACTTGGCGATGCACAAGGTA
CAGAGGCCAGGGGGGAGCAGCCACCTGCAATGGACGCCCCTGCCCTTCTCCCGGCTGGATGAGGGCGCCATGCAGTGGAT
CATGGACCAGGCTGAGGCCAAGATGCAAGGTGCACCCCTAGCCGTGAAGGCTGAGAGGAGGACCACAGGGCCCTCAGGGC
CCCGCCTGACTGCCATACCAGAGCGGTTCAGCGGGCTGCAGGTCAACAGCACCCGCTGGCTGGAAGTCGTGGGCAACTGC
ATCTCCCACGTGTTTGAGAGGAAGATGCCTGAGGCCGAGAAGCTGCTCCCAGCTGTGCTGAGGGCCCTGAAGAGGTGAGC
TGCCTGCTGCTGTCTCGCCGAGGAGCTGCGCCTGCATGTGCAGCAGAACCGGACGGTCGTGGACCACCAGCAGTTTGTGG
TCCGTATGATGAACTGCTGCCTGCAGGACTGCACTTCTCTGGATGAGCATGGCATCTCGGCTGCTCTGCTGCCTCTGGTC
ACAGCCTTCTTGGAAGCTGAGCCAGGGGGGTGAGGCTGTTCTCTTACAGCCCTGTGCAGCAGCAGGTGGTGTGGAGCATG
CCACAATTCTGGGAGGCCATGTTCTGCTGGGACATGAAGACTCACATCTGGGCCCTCTACCTGGAGCCCACTGAGGACCA
GGCCCCCGCCCAGGAGGTTGGGGAGGCACCTTCACAGGAGGACGAG

Alignment

ORF - retro_nleu_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DHTEVFRNSLGLIYAIHVEGLNVCLENVIGNLLTCTVPLAGGSQRTISLGAGDR-QVIQTPLADSLPVSR
          DH.EVFRNS..LIYAIHVEGLNV...NVIGNL.TCTVPLAGGS.R.ISLGAGDR.QVI.TPLADSL..S.
Retrocopy DHAEVFRNSFCLIYAIHVEGLNVFPGNVIGNLPTCTVPLAGGSKRMISLGAGDR<QVIHTPLADSLSISS

Parental  CSVALLFRQLGITNVLSLFCAALTEHKVLFLSRSYQRLADACRGLLALLFPLRYSFTYVPILPAQLLEVL
          CSVALLF.QLGI.N.LSLFCAALTEHKVLF.S.SYQ.LA.ACRGLLALLFP.RYSFTY.PILPAQLLE.L
Retrocopy CSVALLFCQLGIINMLSLFCAALTEHKVLFQSQSYQQLANACRGLLALLFPVRYSFTYGPILPAQLLEAL

Parental  STPTPFIIGVNAAFQAETQELLDVIVADLDGGTVTIPECVHIPPLPEPLQSQTHSVLSMVLDPELELADL
          STPTPFIIGVNAAFQAETQELLDVIVADLDGGTVTIPECVHIPP..EPLQSQTHSVL..VLDPELEL..L
Retrocopy STPTPFIIGVNAAFQAETQELLDVIVADLDGGTVTIPECVHIPPSLEPLQSQTHSVLGTVLDPELELVNL

Parental  AFPPPTTSTSSLKMQDKELRAVFLRLFAQLLQGYRWCLHVVRIHPEPVIRFHKAAFLGQRGLVEDDFLMK
          AFPPPTTS.SSLKMQDKEL.A.FL.LF.QLLQGY.WCLHVVRIHPEPVIRFHKAAFL.Q.GLVEDDFLMK
Retrocopy AFPPPTTSPSSLKMQDKELGALFLWLFDQLLQGYLWCLHVVRIHPEPVIRFHKAAFLAQCGLVEDDFLMK

Parental  VLEGMAFAGFVSERGVPYRPTDLFDELVAHEVARMRADENHPQRVLRHVQELAEQLYKNENPYPAVAMHK
          VLEG.AFA.FVSE.G..Y..TDLFDELV.HEVAR...DE.H...VL.H.QELA.Q.YKNEN.YP..AMHK
Retrocopy VLEGVAFALFVSEHGFLYLHTDLFDELVVHEVARRWVDEKH---VLPHIQELAVQVYKNENLYPDLAMHK

Parental  VQRPGESSHLRRVPRPFPRLDEGTVQWIVDQAAAKMQGAPPAVKAERRTSVPSGPPMTAILERCSGLHVN
          VQRPG.SSHL...P.PF.RLDEG..QWI.DQA.AKMQGAP.AVKAERRT..PSGP..TAI.ER.SGL.VN
Retrocopy VQRPGGSSHLQWTPLPFSRLDEGAMQWIMDQAEAKMQGAPLAVKAERRTTGPSGPRLTAIPERFSGLQVN

Parental  SARRLEVVRNCISYVFEGKMLEAKKLLPAVLRALKGRAARRCLAQELHLHVQQNRAVLDHQQFDFVVRMM
          S.R.LEVV.NCIS.VFE.KM.EA.KLLPAVLRALK..AA..CLA.EL.LHVQQNR.V.DHQQ..FVVRMM
Retrocopy STRWLEVVGNCISHVFERKMPEAEKLLPAVLRALKR*AACCCLAEELRLHVQQNRTVVDHQQ--FVVRMM

Parental  NCCLQDCTSLDEHGIAAALLPLVTAFCRKLSPG-VTQFAYSCVQEHVVWSTPQFWEAMFYGDVQTHIRAL
          NCCLQDCTSLDEHGI.AALLPLVTAF......G.V..F.YS.VQ..VVWS.PQFWEAMF..D..THI.AL
Retrocopy NCCLQDCTSLDEHGISAALLPLVTAFLEAEPGG<VRLFSYSPVQQQVVWSMPQFWEAMFCWDMKTHIWAL

Parental  YLEPTEDPAPAQEVGEAPSQEDE
          YLEPTED.APAQEVGEAPSQEDE
Retrocopy YLEPTEDQAPAQEVGEAPSQEDE

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_558 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007138	1 retrocopy	retro_nleu_2239,
Nomascus leucogenys	ENSNLEG00000026690	1 retrocopy	retro_nleu_558 ,