RetrogeneDB ID: retro_nleu_3002

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397565.1:375436..376065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSNLEG00000010953
• Aliases: None
• Description: None

Sequence

>retro_nleu_3002
GAACAGCCCATCTTCATCACCGGAGCACAGGTCTTCCAGATTGACCCCAACACCGAGAAGAACTGGATGCCTGCAAGCAA
CAGGCGGTCACCATTTCCTGCTTCTGTGATGTCACAAGGAACAGCTGTGGGATCATCAGTGTGGACAGCACCGAGGTGAC
CATAAACAACACAATCACACCGAATAGGACCTTCACCGACACGTCACAGCCGTCTGGGCACTGGGCCGACAGCGGAGCCA
ACACGGTGTTTGGTTTGGGGTTTTCCTCTGAGCAGCAGCTGACAATGTTTGCAGAGAAATTCCAGGAGGTGGAAGAAGCG
GCCAATATAGCCAAAGACAAGACCCAGGAGAACATGGAGCCCTCGAGTAATCATCCTGAGAATCCGGGCGTGGAGCCCCA
TCTTCTACTCCGGCATCCAGCGTCAACGGGACGGATGATGAAAGGCCTCTCAGGCCGCTGCAGCCGACACGCACCTGCAG
TCTGGGAACCACAAGCTGAAGGCGGCGTCGACGCAGAGCGCTGCCCACGGGAGAGGTGGGAGATGGAGCTGCAGACCCGG
CGGGAGAGCGACGCCCGGCTGACCACGGCGCTGCAGGAGTCGGCGGCCAGCGCGGAGCAGAGGAAGAGG

Alignment

ORF - retro_nleu_3002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.72 %
• Parental protein coverage: 59.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EQPIFTTRAHVFQIDPNTKKNWMPAS-KQAVTVSYFYDVTRNSYRIISVDGAKLIL--TLLPNMTVMRNQ
          EQPIF.T.A.VFQIDPNT.KNWMPAS..QAVT.S.F.DVTRNS..IISVD........T..PN.T.....
Retrocopy EQPIFITGAQVFQIDPNTEKNWMPAS<QQAVTISCFCDVTRNSCGIISVDSTEVTINNTITPNRTFTDTS

Parental  MGVGGWAKPLAVAQRYVGEGSWTTLSMFAEKFQEVKEAAKIAKDKTQEKIETSSNHSQ-ESGCETPSSTQ
          ...G.WA...A......G..S...L.MFAEKFQEV.EAA.IAKDKTQE..E.SSNH...ESG...PSST.
Retrocopy QPSGHWADSGANTVFGLGFSSEQQLTMFAEKFQEVEEAANIAKDKTQENMEPSSNHPE<ESGRGAPSSTP

Parental  ASSVNGTDDE-KASHAGPANTHLKSENDKLKIALTQSAANVK-KWEIELQTLRESNARLTTALQESAASV
          ASSVNGTDDE.KAS.A..A.THL.S.N.KLK.A.TQSAA.....WE.ELQT.RES.ARLTTALQESAAS.
Retrocopy ASSVNGTDDE<KASQAAAADTHLQSGNHKLKAASTQSAAHGR<RWEMELQTRRESDARLTTALQESAASA

Parental  EQWKR
          EQ.KR
Retrocopy EQRKR

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_3002 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002 ,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,