RetrogeneDB ID: retro_nleu_1310

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:4862685..4863646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSNLEG00000005608
• Aliases: None
• Description: None

Sequence

>retro_nleu_1310
ATGCCAGAGCTGGCAATACAGAAGGTGGTGGGCCACCCCCGGTGCTGCTTAGCGTGGTGGATCATTTCAACCGAATCGGC
AAGGTTGGAAACCAGAAGCGCGTTGTTGGTGTGTTTTGGGGGTCATGACAAAAGAAAGCAATTGATGTATCGAACAGTTC
TGCAGTTCCTTTTGATGAAGATGACAAAGACAATTCTGTGTGGTTTTTAGATCATGATTATTTGGAAAACATGTGTGGAA
TGTTTAAGAAAGTCAATGCCAGAAAAAGAATAGTTGGCTGGTACCACACAGGCCAGAATATACACAAGAATGACATTACC
ATCAATGAACTCATGAAAAGATACTATCATAACTCAGTATTGATCATTATTGACGTGAATCCAAAGGACCTAGGGCTGCC
CACAGAAGCGTACATTTCAGTGGAAGAAGTCCATGATGATGGAACTCCAACCTTGAAAACATTTGAACACGTGACCAGTG
AAACTGGAGCAGAGTAAGCTGAGGAAGTTGAAGTTAAACACTTGTTATGAGACATCAAAGACACAACGGTGGGCACTCTG
TCCCAGCAGATCACAAACCAGGTCCATGGTTTGAAGGGACTGAACTCCAAGCTTCTGGATATCAGGAGCTACCTGGAAAA
AGTAGCCACAGGCAAGCTGCCCATCAACCACCAGATCATCTACGAGCTGCAGGACGTCTTCAATCTGCTGCCAGACATCA
GCCTGCAGGAGTCTATTAAAGCTTTTTACCTGAGGACCAACGACCAGATGGTGGTAGTGTACTTGGCCTCACTGATCCAT
TCTGTGGTCACCCTGCACAACCTCAACAACAACAAGATTGCCAACCAGGATGGAGACAAGAAAGAAGGGCAGGAGAAAGA
AGAGAGCAAAAAGATAGAAAAGCTGACAAGGGGAAAGATAAAGTTAAGGAAAAGAGTGATGTAAAGAAAGAGGAGAAAAA
G

Alignment

ORF - retro_nleu_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.69 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPELAVQKVVVHPL-VLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWF
          MPELA.QKVV.HP..VLLSVVDHFNRIGKVGNQKRVVGV..GS.QKK..DVSNS.AVPFDEDDKD.SVWF
Retrocopy MPELAIQKVVGHPR<VLLSVVDHFNRIGKVGNQKRVVGVFWGS*QKKAIDVSNSSAVPFDEDDKDNSVWF

Parental  LDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYI
          LDHDYLENM.GMFKKVNAR.RIVGWYHTG...HKNDI.INELMKRY..NSVL.IIDV.PKDLGLPTEAYI
Retrocopy LDHDYLENMCGMFKKVNARKRIVGWYHTGQNIHKNDITINELMKRYYHNSVLIIIDVNPKDLGLPTEAYI

Parental  SVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIR
          SVEEVHDDGTPT.KTFEHVTSE.GAE.AEEV.V.HLL.DIKDTTVGTLSQ.ITNQVHGLKGLNSKLLDIR
Retrocopy SVEEVHDDGTPTLKTFEHVTSETGAE*AEEVEVKHLL*DIKDTTVGTLSQQITNQVHGLKGLNSKLLDIR

Parental  SYLEKVATGKLPINHQIIYQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNK
          SYLEKVATGKLPINHQIIY.LQDVFNLLPD.SLQE..KAFYL.TNDQMVVVYLASLI.SVV.LHNL.NNK
Retrocopy SYLEKVATGKLPINHQIIYELQDVFNLLPDISLQESIKAFYLRTNDQMVVVYLASLIHSVVTLHNLNNNK

Parental  IANRDAEKKEGQEKEESK-KDRKEDKEKDKDKEKSDVKKEEKK
          IAN.D..KKEGQEKEESK.KDRK.DK.KDK.KEKSDVKKEEKK
Retrocopy IANQDGDKKEGQEKEESK<KDRKADKGKDKVKEKSDVKKEEKK

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_1310 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310 ,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,