RetrogeneDB ID: retro_nleu_3040

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397613.1:265459..266459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSNLEG00000013733
• Aliases: None
• Description: None

Sequence

>retro_nleu_3040
GAAGGGGCCCAGCCTGTTGACAAGGGGAACAGGCCGCCGGCCCTGAGCGGGACCCGGGTTCCGGCCTGCAAGACTGCAAG
GAGGATCTTTCATGAGCCTTCGAGCCGAAAATTAAAGCAGCTGCCCCCGGCGTGGAGGATGAGCCTCTGCTGAGAGGAAA
CCCCTGCCACTTTGTCGTCTTCCCCATCGAGTACCATGATATCTGGCAGATGTATAAAAAGGCAGAGGCTTCCTTCTGGA
CCACCGAGGAGGTGGACCTGTCCAAGGACATTCAGCACTGGGAATCCCTGAAGCCCGAGGAGAGATATTTTATATCCCGT
CTTCTGGTTTTCTTTGCAGCAAGTGATGGCATAGTAAATGAAAATTTGGTGGAGCGATTTAGCCAAATAGTTCAGATTAC
AGAAGCCTGCTGTTTCTATGTCTTCCAAATTGCCATGGAAAACATACATTCTGAAATGTATAGTCTCCTTATTGACACTT
ACATCAAAGATGCCAAAGAAAGGGAATTTCTCTTTAATGCCATCGAAACGATGCCTTGCGTCAAGAAGAACGCAGATTGA
GCCTTGTGCTGGATTGGGGACAAAGAGGCTATCTATGGTGAACGTGTTGTAGCCTTTGCTGCAGTAGAAGGCATCTTCTT
TTCCGGTTCTTTTGCATCGATATTGTGGCTCAAGAAACGAGGACTGATGCCTGGCCTCACGTTTTCGAATGAACTTATTA
GCAGAGATGAGGGTTTACACTGTGATTTTGCTGCTTGATGTTCAAATACCTGGTGCACAAACCATCGGAGGAGAGAGTGA
GAGAAACAATTATCAATGCTGTTCAGATAGAACAGGAATTCCTCACTGAGGCCTTGCCTATGAAGCTCATTGGGATGAAT
TGCACTCTAATGAAGCAATGCATTGAGTTTGTGGCAGGCAGACTTAGGCTGGAACTGGGTTTTAGTAAGGTTTTCGGGGT
AGAGAGCCCATTTGACTTTATGGAGAATATTTCACTGAAA

Alignment

ORF - retro_nleu_3040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 76.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGLSLVDKENTPPALSGSRVLASKTARRIFQEPA-EPKTKAAAPGVEDEPLLRENPRRFVIFPIEYHDIW
          .G...VDK.N.PPALSG.RV.A.KTARRIF.EP..EPK.KAAAPGVEDEPLLR.NP..FV.FPIEYHDIW
Retrocopy EGAQPVDKGNRPPALSGTRVPACKTARRIFHEPS<EPKIKAAAPGVEDEPLLRGNPCHFVVFPIEYHDIW

Parental  QMYKKAEASFWTAEEVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCF
          QMYKKAEASFWT.EEVDLSKDIQHWESLKPEERYFIS..L.FFAASDGIVNENLVERFSQ.VQITEA.CF
Retrocopy QMYKKAEASFWTTEEVDLSKDIQHWESLKPEERYFISRLLVFFAASDGIVNENLVERFSQIVQITEACCF

Parental  YGFQIAMENIHSEMYSLLIDTYIKDPKEREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAV
          Y.FQIAMENIHSEMYSLLIDTYIKD.KEREFLFNAIETMPCVKK.AD.AL.WIGDKEA.YGERVVAFAAV
Retrocopy YVFQIAMENIHSEMYSLLIDTYIKDAKEREFLFNAIETMPCVKKNAD*ALCWIGDKEAIYGERVVAFAAV

Parental  EGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFA-CLMFKHLVHKPSEERVREIIINAVRIE
          EGIFFSGSFASI.WLKKRGLMPGLTFSNELISRDEGLHCDFA.CLMFK.LVHKPSEERVRE.IINAV.IE
Retrocopy EGIFFSGSFASILWLKKRGLMPGLTFSNELISRDEGLHCDFA<CLMFKYLVHKPSEERVRETIINAVQIE

Parental  QEFLTEALPVKLIGMNCILMKQYIEFVADRLMLELGFGKVFRVENPFDFMENISLE
          QEFLTEALP.KLIGMNC.LMKQ.IEFVA.RL.LELGF.KVF.VE.PFDFMENISL.
Retrocopy QEFLTEALPMKLIGMNCTLMKQCIEFVAGRLRLELGFSKVFGVESPFDFMENISLK

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_3040 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 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040 ,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,