RetrogeneDB ID: retro_nleu_1964

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397319.1:4027800..4028406(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSNLEG00000010969
• Aliases: None
• Description: None

Sequence

>retro_nleu_1964
ATGGAGAATGGATACACATATGAAGATTACCAGAGCACTGCAGAGCGGCTTCTGTTTCACACCAAGCACTGAACACAAGT
GACAGTGATCTGTGGGTCTGAATTAGGAGATCTGACTGACAAATTAATTCAGGCCCAAATCTTCAACAACAGTGAGATGC
TCAACTTTCTCCAAAGTACAGTGCCAGGTCATGCTGGTCGACTGGTGTTTGGGTTCCTGAATGGCACAGCGTGTGTGATG
ATGCAAGGAAGGTTCTACTTGTATGATGGGCACCTGCTCTGGAACACGACATTTTTGCATGAGGTTTTCCAGCTTCTGGG
CGGGAACATCTTGGTGGCCACCGATGCAGCTGGAGGGCTCAACCCCAAGTCTGAGGTTGGAAGGATCATGCTTCTCTGTG
ATCACACCAAGCTACTTGGTTTCTGTGATCAGAACTCTCCCAAAGGGCCCAATGATGAAAGGTTTGGAGTTCATTTTCCT
GCCACATCTGATGCCTACAACTGGACAATGAGGCAAAAGGCGCTCAATTCGTAGAACCAAATGGGGAAGCAGCAAGAGGT
ACAGAAAGACATCTGTGTGATGGCAGTAAACCACAACTTTGAGACT

Alignment

ORF - retro_nleu_1964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.05 %
• Parental protein coverage: 70.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGSLTDKLTQAQIFDYSEIPNFPRSTVPGHAGRLVF
          MENGYTYEDY..TAE.LL.HTKH..QV..ICGS.LG.LTDKL.QAQIF..SE..NF..STVPGHAGRLVF
Retrocopy MENGYTYEDYQSTAERLLFHTKH*TQVTVICGSELGDLTDKLIQAQIFNNSEMLNFLQSTVPGHAGRLVF

Parental  GFLNGRACVIMQGRFHMYEGYSLWKFASKVTFPVRVFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHI
          GFLNG.ACV.MQGRF..Y.G..LW......TF...VF.LLG...LV.T.AAGGLNPK.EVG.IML..DH.
Retrocopy GFLNGTACVMMQGRFYLYDGHLLW----NTTFLHEVFQLLGGNILVATDAAGGLNPKSEVGRIMLLCDHT

Parental  NLPGFSGQNPLRGPNDERFGVRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFET
          .L.GF..QN...GPNDERFGV.FPA.SDAY..TMRQ.AL....QMG.Q.E.Q....VM.....FET
Retrocopy KLLGFCDQNSPKGPNDERFGVHFPATSDAYNWTMRQKALNS*NQMGKQQEVQKDICVMAVNHNFET

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_1964 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.

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964 ,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,