RetrogeneDB ID: retro_nleu_2012

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:254568..255044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSNLEG00000013804
• Aliases: None
• Description: None

Sequence

>retro_nleu_2012
ATCAATAAAGTAGAAACTGCTGTCAAGTAGGATGAGATCCAGATAAAGATCTGGAGGTGCTCGTATGATATCCTACCACC
TCCGATAAGCCCTGGCCATTCTTTCTACAGCAACATCAGTGAGGATCACAGACATGAAGACCTCACTGAAGACCAGCTAG
CACCCTGTTAAAGCCTGAGGGACATTACTGCCAGAGTTCTGCCCTTTTGGATAGAAGTAATACTTCCTCAGATTAAGGAA
GGGAACTGGACACCGATTGTGGTCCATGGAACAGCCTTCAGGGAATTGTCAAGCATAGGGAGGGTCGCTCTGAAGAAGCT
ACCACAGAGCTTAGTCTGCAGACTAGTATTCTTGTTGTTTATGAATTGAATTGGGAGAAGAACTTAAAGCCCTTCAAACA
TATGCAGTACCTAGGAAACGAGGAGGCCATGTATGAAGCCATACAAGCTGTAACTGCCAAGGGCATGGTCAAGGAG

Alignment

ORF - retro_nleu_2012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.62 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFW
          .NK.ETA.K..E.Q.KIWR.SYD..PPP..P.H.FYSNIS.D.R..DLTEDQL..C.SL.D..AR.LPFW
Retrocopy INKVETAVK*DEIQIKIWRCSYDILPPPISPGHSFYSNISEDHRHEDLTEDQLAPC*SLRDITARVLPFW

Parental  NEEIVPQIKEGKRVLIAAHG-NSLRGIVKHLEGLSEEAIMELNLPTGIPIVYEL--DKNLKPIKSMQFLG
          .E.I.PQIKEG....I..HG.NSL.GIVKH.EG.SEEA..EL.L.T.I..VYEL...KNLKP.K.MQ.LG
Retrocopy IEVILPQIKEGNWTPIVVHG<NSLQGIVKHREGRSEEATTELSLQTSILVVYELNWEKNLKPFKHMQYLG

Parental  DEETVRKAMEAVAAQGKAKK
          .EE....A..AV.A.G..K.
Retrocopy NEEAMYEAIQAVTAKGMVKE

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_2012 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 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Nomascus leucogenys	ENSNLEG00000013804	10 retrocopies	retro_nleu_1367, retro_nleu_1535, retro_nleu_1658, retro_nleu_2012 , retro_nleu_2139, retro_nleu_2196, retro_nleu_2205, retro_nleu_2488, retro_nleu_2667, retro_nleu_280,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,