RetrogeneDB ID: retro_nleu_1335

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397289.1:5363521..5364182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSNLEG00000014704
• Aliases: None
• Description: None

Sequence

>retro_nleu_1335
TGTCAGCTTCCTGGTGTCTTTAATTGTGCTTAGCATATTATGAGCATCAGTTGGAGGCCTTAGTACATTGTAAGCATCAA
CTCCAAGGCTGTGTTCAGGAGTCCTTAGAAATATGATTCACAGTAAAGTTTTACAGCATTACCAGGAATGTGACAAGATT
GAGGAGTTAGGACCTGGTAATGTGCAGAAAGAAGTCTCATCTTCCTTTGACCAAGTTATCAAGAAGGCAATTTGAGAGAT
AATCACTCATTTTGCTGCTGTCCTCATCACAAATCCCTTCCATATTATCACCGAGGTACAATTCATTGGCAGAGAACCGA
AGTACTGCAGACTTTGTGACTCCATAGCAACCATCTATTAGGGAGAGGGCATCCTAGGATTTTTCATGGGTCTTGTGCCT
CAGCTCCAAGGTGACATCATTTCTTTGTGGCTCTGTAACTCACTGGCTTGCCTCATCAATATCTATGTACTGAACAGTGG
GGATTCCACCATGAATGAAATAAAGAATTATTCCCAAGTTGTTACAGAAACTTGTGCCAATATGTTGAGCTAATCTCTTG
TGTTTGTCTGTAATTTTATGTCTGTCGACAGCCGAAGGCTTGCTGGTGAAGCCCCTCCTTATTGCCCAATGTATACTTCT
TGCATAGATTGTTGGCGCATG

Alignment

ORF - retro_nleu_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.73 %
• Parental protein coverage: 81.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CQLPGLFSYAQHIASIDGRRGLFTGL-TPRLCSGVLGTVVHGKVLQHYQESDKGEELGPGNVQKEVSSSF
          CQLPG.F..A.HI.SI..R........TPRLCSGVL....H.KVLQHYQE.DK.EELGPGNVQKEVSSSF
Retrocopy CQLPGVFNCA*HIMSISWRP*YIVSI>TPRLCSGVLRNMIHSKVLQHYQECDKIEELGPGNVQKEVSSSF

Parental  DHVIKETTREMIARSAATLITHPFHVITLRSMVQFIGRESKYCGLCDSIITIYREEGILGFFAGLVPRLL
          D.VIK....E.I...AA.LIT.PFH.IT....VQFIGRE.KYC.LCDSI.TIY..EGILGFF.GLVP.L.
Retrocopy DQVIKKAI*EIITHFAAVLITNPFHIIT---EVQFIGREPKYCRLCDSIATIY*GEGILGFFMGLVPQLQ

Parental  GDILSLWLCNSLAYLVNTYALDSGVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLMAVNNCGLAGGCPP
          GDI.SLWLCNSLA.L.N.Y.L.SG.STMNE.K.YSQ.VT...A.ML....V.V.N.M.V....LAG..PP
Retrocopy GDIISLWLCNSLACLINIYVLNSGDSTMNEIKNYSQVVTETCANMLS*SLVFVCNFMSVDSRRLAGEAPP

Parental  FSPIYTSWIDCWCM
          ..P.YTS.IDCW.M
Retrocopy YCPMYTSCIDCWRM

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_1335 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335 , retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,