RetrogeneDB ID: retro_nleu_582

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:34724875..34726639(-)
• Located in intron of: ENSNLEG00000005173

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCAPG
• Ensembl ID: ENSNLEG00000016632
• Aliases: None
• Description: None

Sequence

>retro_nleu_582
AAAATGCTGGCTATTTGACAGGAGATTCTTACTCTACCCACAACCCCAATATCCCTGGTTCCTTTTCTTGAAGGACTGCT
CCACATTATTCTAGATGATAATAAGAGAACGGAATTTATCTCAGAGATTGGGGCACCCATTGTTACTGTTGGTGTTAATG
ATGACCCAGCTGATGCAAGAAAGGAAGGACTCAAGATGGCTGAAATAAAAGTTAAGCATATTGAAGCCAAAGAAGCTTTG
GAAAATTACATTACCTTACAGGATTTTAACTCGGCATCAAAATTAAAAGAAGAAATAAGAGGATTAGAAGATGTCAAAAA
AACCTTTTGTAAGAGACAGAGCAACTTGAAATTAAAGAAGTCCATGTAGAGAAGAATGACACAGAAACATTACAGAATCT
CTTATCTTATGCTGTGAACTGTTAAAGCAGATGTCCATTTCAACAGGCATAAGTGCAGCCATGAATGGGATCATCGAATT
TTTTATTCTTCCTAAAATAATAAATGTTTACCCTATAGTAAGAAACTTGGCTGTTTCATGCTCGGGAGCTGCAGACTACA
GAATCAGAATTTTGCACGTAACACTTTGTGTTATTATTGCAGGTTTTGCAAATTGATGATGTCACAATAAAAATAAGTGC
TTTAAAGGGAATCTTTGACTAGCTGATAATGTTTGGGGTTGAACCACTTAAACCTAAAAAATCAAAGCCTTTTAATTTGA
AGGTGCAGAGATAAACAGTGATTGATGAGCAAGAGTCATAAAAAGTTGAAAAGGCCCTTACAGCGAAGAGTGTTCTGAAA
CTCCTTTCTGATTTCTTAGGTAGTGAGGTGTCTACACTTAGGACAGGAGCCACAGAAGGATTAGCCAAGCTGATATTCTC
TGGGCTTTTGGTGAGCAGCAGGACTTTTTCCCATCTTATTTTGTTATGGTAGAGTCCTGTGACTGAAGAGGATGTTCGAC
TTCGACATTGCCTAGGCATGTTCTCCCCCATGTTTGCTTAGGCAAGCAGGACTAATCAGGAATGCTTTGAAGAAGTTTCT
CTTCCAAGCCTGCAAACACTGGCCAATGCTCCTGCATCTTCTCCTTTAGCTGAAATTGATATCAGAAATGTTGTTGAGTT
ACTTACAGATTTGACAAGAACAAGTAGATTAAATCCTCAGGCCAAGAATTCCTAAGATTATCAGGCCTTAACAGTACATG
ACAATTTGGCTATAAAAATTTGCAGTGATATCTTAAGAAGTCCATGCTCACCAGAAATTCAGGTCTCTATAAAAGCCTTG
AGTTCTTTAGAACTCAATAGCCATCTTGCAAAAGATCTTCTGGTTCTATTGAATGGGATTCTGGAGCAAGTAAAGGAGAC
GGCATGTCTGAAAGCTTTGGAGAAAATCAAGATTCAGTTAGCAAAAAGGAAATAAAGAATTTGGTGACCAGCCTGAAGCA
GCACAGGATGCCAGCTTGACTACAACTATTTTTCAAAATGAAGATAAAAAGAATAAGGAAGTACATATGACTCTTCTTAG
GGATGTAAAAGCAACCCTGGCATCAAAATCTACTCAGCAAAAGACTAACAGGGGACAGAGAAAAGTCACAGCTTCAGCTA
GGATGAAGAGGAGACATCAGATTGCTGAGGCTGACTCTGAAAGTGACCATGAAATTCTAGAACCAGAATCAGAAATGAAG
ATGAAACTACCAAGGCAAGCCAGAACAGCAGTGCTGGAAAAAAGTAAACTTAATCTTGCCCAACTTCTCAATGAAGATAG
AAGT

Alignment

ORF - retro_nleu_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 58.52 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KLLAVLQEILILPTIPISLVSFLVERLLHIIIDDNKRTQIVTEIISEIRAPIVTVGVNNDPADVRKKELK
          K.LA..QEIL.LPT.PISLV.FL.E.LLHII.DDNKR....TE.ISEI.APIVTVGVN.DPAD.RK..LK
Retrocopy KMLAI*QEILTLPTTPISLVPFL-EGLLHIILDDNKR----TEFISEIGAPIVTVGVNDDPADARKEGLK

Parental  MAEIKVKLIEAKEALENCITLQDFNRASELKEEIKALEDARI-NLLKETEQLEIKEVHVEKNDAETLQ-K
          MAEIKVK.IEAKEALEN.ITLQDFN.AS.LKEEI..LED....NLL.ETEQLEIKEVHVEKND.ETLQ..
Retrocopy MAEIKVKHIEAKEALENYITLQDFNSASKLKEEIRGLEDVKK<NLL*ETEQLEIKEVHVEKNDTETLQ<E

Parental  CLILCYELLKQMSVSTGLSATMNGIIESLILPGIISIHPVLRNLAVLC-LGCCGLQNQDFASK-HFVLLL
          .LILC.ELLKQMS.STG.SA.MNGIIE..ILP.II...P..RNLAV.C.LG.C.LQNQ.FA...HFVLLL
Retrocopy SLILCCELLKQMSISTGISAAMNGIIEFFILPKIINVYPIVRNLAVSC<LGSCRLQNQNFARN<HFVLLL

Parental  QVLQIDDVTIKISALKAIFDQLMTFGIEPFKTK-KIKTLHCEGTEINSD-DEQESKEIEETATAKNVLKL
          QVLQIDDVTIKISALK.IFD.L..FG.EP.K.K.KIK....EG.EINSD.DEQES...E...TAK.VLKL
Retrocopy QVLQIDDVTIKISALKGIFD*LIMFGVEPLKPK<KIKAF*FEGAEINSD>DEQES*KVEKALTAKSVLKL

Parental  LSDFLDSEVSELRTGAAEGLAKLMFSGLLVSSRILSRLILLWYNPVTEEDVRLRHCLGVFFPVFAYASRT
          LSDFL.SEVS.LRTGA.EGLAKL.FSGLLVSSR..S.LILLW..PVTEEDVRLRHCLG.F.P.FA.ASRT
Retrocopy LSDFLGSEVSTLRTGATEGLAKLIFSGLLVSSRTFSHLILLW*SPVTEEDVRLRHCLGMFSPMFA*ASRT

Parental  NQECFEEAFLPTLQTLANAPASSPLAEIDITNVAELLVDLTRPSGLNPQAKTSQDYQALTVHDNLAMKIC
          NQECFEE..LP.LQTLANAPASSPLAEIDI.NV.ELL.DLTR.S.LNPQAK.S.DYQALTVHDNLA.KIC
Retrocopy NQECFEEVSLPSLQTLANAPASSPLAEIDIRNVVELLTDLTRTSRLNPQAKNS*DYQALTVHDNLAIKIC

Parental  NEILTSPCSPEIRVYTKALSSLELSSHLAKDLLVLLNEILEQVKDRTCLRALEKIKIQL-EKGNKEFGDQ
          ..IL.SPCSPEI.V..KALSSLEL.SHLAKDLLVLLN.ILEQVK...CL.ALEKIKIQL..KGNKEFGDQ
Retrocopy SDILRSPCSPEIQVSIKALSSLELNSHLAKDLLVLLNGILEQVKETACLKALEKIKIQL>QKGNKEFGDQ

Parental  AEAAQDASLTATTFQNEDEKNKEVYMTPLRGVKATQASKSTQLKTNRGQRKVTVSARTNRRRQTAEADSE
          .EAAQDASLT.T.FQNED.KNKEV.MT.LR.VKAT.ASKSTQ.KTNRGQRKVT.SAR..RR.Q.AEADSE
Retrocopy PEAAQDASLTTTIFQNEDKKNKEVHMTLLRDVKATLASKSTQQKTNRGQRKVTASARMKRRHQIAEADSE

Parental  SDHEVPEPESEMKMRLPRRAKTAALEKSKLNLAQFLNEDLS
          SDHE..EPESEMKM.LPR.A.TA.LEKSKLNLAQ.LNED.S
Retrocopy SDHEILEPESEMKMKLPRQARTAVLEKSKLNLAQLLNEDRS

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_582 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000018070	1 retrocopy	retro_mmul_2370,
Nomascus leucogenys	ENSNLEG00000016632	1 retrocopy	retro_nleu_582 ,
Pongo abelii	ENSPPYG00000014630	1 retrocopy	retro_pabe_3369,