RetrogeneDB ID: retro_nleu_2239

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397337.1:11053691..11055087(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTMR2
• Ensembl ID: ENSNLEG00000007138
• Aliases: None
• Description: None

Sequence

>retro_nleu_2239
GCCTCCACTTCTCATTCAGAGAATTCAGTGCATACAAAATCAGCTTCTGTTGTATCATCAGATTCCATTTCAACTTCTGC
CAACAACTTTTCTCCTGATTTTAGGGTCCTAAGGGGGCCTAACAAGTTAGCAGAAATGGAAGAACCACCCTTGCTTCAAG
GAGAAAATATTAAAGACATGGCCAAAGATGTAACTTGTATATGTCCATTCACTGGTCTTGCACGAGGAATTCTGACTGAC
ACAAATCATAGGTTATACTTCAAAACCGTGGGACGGGATCCCCCAATTTTTTTAGATGCTTCTCTTGGTGTGATAAGTAG
AGTAGAAAAAATTTGTGGTGCTTCTAGTCGAGGTGAAAATTTTTATGGACTAGAAACTGTGTCTAAGGATATTAGGAATG
TATGATATGCTCATAAACCTGAGGGGCAAACAAGAATATCCATATTTGAGAATCTAATGAAATATGCATCTCCTGTCTCT
AATAACCTGCCTCTTTTTGCTTTTGAATACAAAGAAGTATTCCCTGAAAATGGGTGGAAGCTATATATATACTATTTTGG
AGTATAGAAGGCAGGGAATTCCAAATGAAAGGTGGAGAATAACAAAGATAAATGAACGATATGAACTTTGTGATACATAC
CCTGCCCTCCTGGTTGTGCCAGCAAATATTCCTGATGAAGAATTAAAGAGAGTGGCATTCTTCAGATCAAAAGGACATAT
CCCAATTTTATCATGGAGTCATCCTGAAAGTCAAGCCACAGTCACTCGGTGTAGCCAGCCGACGGTTAGAGTGAGTGGAA
AGCGAAACAAAGATGAAAAATACCTTCAAGCTATCATGGATTCCAATGCCCAATCTCACAAAGTCTTTATATTTGATGCC
CAGCCAAGTGTTAATGCTGTTGCCAATAAGGCAGAGGGTGGAGGTTATGAAAGTGAAGATGCCTATCAAAATGCTGAACT
AGTTTTTCTGGATATCCACGATATTCGTGTTATGAGAGAATCATTACAAAAACTTAAGGCGATTGTGTACGCCAACATTG
GGGAAACTCACTGGTTGTCTAACACGGAATCTACTCATTGGCTAGAACATATTAGGCTTATGCTTGCAGGGGCTCTTAGG
ATTGCTGACAAGGTAGAGTCAGGGAAGATGTCTGTGGTAGTGCATTGCAGTGATGGCTGGGATCGCACAACTCAGCTCAC
TTCCCTTACCATGCTCATGTTGGGTGGATACTATCGAACCATCCGAGGATTTAAAGTCCTTGTGGAGAAAGAATGGCTAA
GCTTTGGACATGGATTTCAAGTAAGAGTTGGCCATGGAGATAAGAACGATGCAGATGCAGACAGATCACCTGTTTTTCTT
CAATTTATTGACTCTGTCTGGCAGATGACAAGACAG

Alignment

ORF - retro_nleu_2239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.15 %
• Parental protein coverage: 75.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASTSHSENSVHTKSASVVSSDSISTSADNFSPDLRVLRESNKLAEMEEPPLLPGENIKDMAKDVTYICPF
          ASTSHSENSVHTKSASVVSSDSISTSA.NFSPD.RVLR..NKLAEMEEPPLL.GENIKDMAKDVT.ICPF
Retrocopy ASTSHSENSVHTKSASVVSSDSISTSANNFSPDFRVLRGPNKLAEMEEPPLLQGENIKDMAKDVTCICPF

Parental  TGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP
          TG..RG.LT.TN.RLYFK...RDPP..LDASLGVISRVEKI.GASSRGEN.YGLETV.KDIRN...AHKP
Retrocopy TGLARGILTDTNHRLYFKTVGRDPPIFLDASLGVISRVEKICGASSRGENFYGLETVSKDIRNV*YAHKP

Parental  EGRTRRSIFENLMKYAFPVSNNLPLFAFEYKEVFPENGWKLYD-PLLEYRRQGIPNESWRITKINERYEL
          EG.TR.SIFENLMKYA.PVSNNLPLFAFEYKEVFPENGWKLY....LEYRRQGIPNE.WRITKINERYEL
Retrocopy EGQTRISIFENLMKYASPVSNNLPLFAFEYKEVFPENGWKLYI>TILEYRRQGIPNERWRITKINERYEL

Parental  CDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATVTRCSQPMVGVSGKRSKEDEKYLQAI
          CDTYPALLVVPANIPDEELKRVA.FRS.G.IP.LSW.HPESQATVTRCSQP.V.VSGKR.K.DEKYLQAI
Retrocopy CDTYPALLVVPANIPDEELKRVAFFRSKGHIPILSWSHPESQATVTRCSQPTVRVSGKRNK-DEKYLQAI

Parental  MDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEE
          MDSNAQSHK.FIFDA.PSVNAVANKA.GGGYESEDAYQNAELVFLDIH.I.VMRESL.KLK.IVY.NI.E
Retrocopy MDSNAQSHKVFIFDAQPSVNAVANKAEGGGYESEDAYQNAELVFLDIHDIRVMRESLQKLKAIVYANIGE

Parental  THWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHCSDGWDRTAQLTSLAMLMLDGYYRTIRGFE
          THWLSN.ESTHWLEHI.L.LAGALRIADKVESGK.SVVVHCSDGWDRT.QLTSL.MLML.GYYRTIRGF.
Retrocopy THWLSNTESTHWLEHIRLMLAGALRIADKVESGKMSVVVHCSDGWDRTTQLTSLTMLMLGGYYRTIRGFK

Parental  VLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQ
          VLVEKEWLSFGH.FQ.RVGHGDKN.ADADRSPVFLQFID.VWQMTRQ
Retrocopy VLVEKEWLSFGHGFQVRVGHGDKNDADADRSPVFLQFIDSVWQMTRQ

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_2239 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000031918	3 retrocopies	retro_mmus_3004, retro_mmus_3005, retro_mmus_3006,
Nomascus leucogenys	ENSNLEG00000007138	1 retrocopy	retro_nleu_2239 ,
Nomascus leucogenys	ENSNLEG00000026690	1 retrocopy	retro_nleu_558,
Nomascus leucogenys	ENSNLEG00000026811	2 retrocopies	retro_nleu_2491, retro_nleu_557,