RetrogeneDB ID: retro_nleu_1963

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397319.1:3868709..3869804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSNLEG00000002948
• Aliases: None
• Description: succinate-CoA ligase, ADP-forming, beta subunit [Source:HGNC Symbol;Acc:11448]

Sequence

>retro_nleu_1963
ATGGTGGCCTTCATGTTCTATAGCTGACAATTAGCTGCTGCTGTTCACAGCCATCAGTCCCAGACTAGACCATAGTACAG
TCTACTGCCCAGGTTCTGGGAATTTCTGAACTGTTTAATAACCAATAACTCCAAGTACAGCAGCAACAGCAAAAGAATCT
CTCACTACATGAATATATGAATATGAAATTGTTGCAAGAAGCTGGTGTCTCCCTTCCAAAGGATATGTGGCAAAGTCACC
AGATGAAGCTGACGCAATTGTCAAAAAATTAGGTTCTAAAGATGTGATAATGGCACAGAATTTTGCTTGCGGTAGAGAAA
AAGGAACATTTGAAAGCAGTCCCAAAAGAGGAGTGAAGATAGTTTTCTATCAAGAAGCAAAAGCTGTTTCCTCTCAAATT
ATTGGGAAAAAGTTGTTTACCAAGTAAACAGGAGAAAAGGACAAAATATGCAATCAAGTATTGATCTGTGAGCAAAAATA
TCCCAGAGAGAATACTACTTTCCAGTAACAATGGAAAGGTCATTTCAAGGTCTAGTATAAATAGGAAGTTTGCAAGGTGG
TGTCAACACTGAAGATGTTTCTGCTGAGACTCCTGATGTAATAAAGAAGCTATTGATGTCGTAGAAGGCATCTAAAAGGA
ACAAGCTCTCCAGCTTGCATAGAATATAAGATTTCCATCTACTACTGTGGATTCTGTGGCAGAAAACATGGTCAAGCTTT
ACAACCTTTTTCTGAACTACAACACAACCATGATAAAAATAAGCCCAACGGTATAAGATTCAGATGGAGTTCTGCTATGT
TTGGACACAAAGATCAATTTTGATTCTAATTCAGTCTATTGCCAGAAGATCTTTGATCTACAGGACTGGACTCAGGAAGA
TGAAAGGAACAAAGATGAAGCTAAGCCACATCTCAATAACATTGGCCTCAGTGGAAAAACAGGCTGTCTAGTAAACGGTG
CTGGTTTGGCTATAACCACAATAGATATAAGAAAACTTCATAAAGAGACTCCAACCAGCTTCCTTGTTGTTCATGGCAGT
GCTATATTTCCATCAAGTAACAGAATCATTTATGCTTATCACTTCAGATAAAAAG

Alignment

ORF - retro_nleu_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAASIFYG-RLVAVATLRNHRPR-TAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAG
          M.A..FY...L.A.........R.T.....AQVLG.S.LFNN..LQVQQQQQ.NLSLHEYM.M.LLQEAG
Retrocopy MVAFMFYS*QLAAAVHSHQSQTR<TIVQSTAQVLGISELFNNQ*LQVQQQQQKNLSLHEYMNMKLLQEAG

Parental  VSVP-KGYVAKSPDEAYAIAKKLGSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIG
          VS.P.KGYVAKSPDEA.AI.KKLGSKDV...AQ..A.GR.KGTFES..K.GVKIVF...EAKAVSSQ.IG
Retrocopy VSLP<KGYVAKSPDEADAIVKKLGSKDVIM-AQNFACGREKGTFESSPKRGVKIVFY-QEAKAVSSQIIG

Parental  KKLFTKQTGEKGRICNQVLVCERKYPR-REYYFAIAMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIK-
          KKLFTK.TGEK..ICNQVL.CE.KYPR.REYYF...MERSFQG.V.IGS..GGVN.EDV.AETP...IK.
Retrocopy KKLFTK*TGEKDKICNQVLICEQKYPR<REYYFPVTMERSFQGLV*IGSLQGGVNTEDVSAETPD-VIK<

Parental  EPIDIEEGIKKEQALQLAQKMGFPPNIVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKI
          E.ID..EGI.KEQALQLA....FP...V.S.AENMVKLY.LFL.Y..TMI.I.P.V.DSDG..LC.D.KI
Retrocopy EAIDVVEGI*KEQALQLA*NIRFPSTTVDSVAENMVKLYNLFLNYNTTMIKISPTV*DSDGVLLCLDTKI

Parental  NFDSNSAYRQKKIFDLQDWTQEDERDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANF
          NFDSNS.Y.Q.KIFDLQDWTQEDER.KD.AK..LN.IGL.G..GCLVNGAGLA..T.DI.KLH..TP..F
Retrocopy NFDSNSVYCQ-KIFDLQDWTQEDERNKDEAKPHLNNIGLSGKTGCLVNGAGLAITTIDIRKLHKETPTSF

Parental  LDVGGGAT-VHQVTEAFKLITSDKK
          L.V.G.A...HQVTE.F.LITSDKK
Retrocopy LVVHGSAI>FHQVTESFMLITSDKK

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_1963 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963 , retro_nleu_2140, retro_nleu_2302,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,