RetrogeneDB ID: retro_nleu_1480

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397295.1:9035101..9035731(-)
• Located in intron of: ENSNLEG00000008719

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSNLEG00000004150
• Aliases: None
• Description: None

Sequence

>retro_nleu_1480
CAAGAACTCCAGTCAGTTGTGAATGATAAGAGCCAGGACCTCCAGAGGCTGCAGGCACAAATGAATGAACTAAATGCAAA
AGTTCACCTATTGCAGGAGGAGCTACAGCTGCTGCAGTAACAGGGCTCCTGTATGAGGGAAGTAGTCCAGGTCATGGATA
AGGAGAAAGTGTTAGTCAAGGTGTATCCCAAGGGCAAGTTTGTCTTAGATGTGGACAGAAACAGCGACATCAATGACATG
AGACCCAATTGCCAGGGGGCACTAAGAAATGATAGCTACACACTGCACAATATCATACCCAGCAAAGTAGACCCACTGGT
GTCACCAGTGATGGTGGAGAAGGTGCCAACCTTGATTTAAGAGATGATTGGTGGACTGGACAAGCAGATTAAGGACATCA
CAGAAGTGATCGAGCCGCCTGTTAAGCATCCCAACCTCTTTGAAGCACTGGGTATCACACAACCCAGGGTGGTACCACTG
TATGGACCTCTAGGCACTGGGAAGACACCGTTTGCCTAGGCTGTGGCTCACCATACAGACTGTACGTTTGTTCATATCCC
TGGCTCTGAATTGGTATAGAAATTCATCAGGGAAGGGCCAAGAATGGTGAGGGAGCTGTTTGTCATGGCA

Alignment

ORF - retro_nleu_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.24 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVD
          .ELQ..VNDKSQ.L.RLQAQ.NELNAKV.LL.EELQLLQ.QGS...EVV..MDK.KVLVKV.P.GKFV.D
Retrocopy QELQSVVNDKSQDLQRLQAQMNELNAKVHLLQEELQLLQ*QGSCMREVVQVMDKEKVLVKVYPKGKFVLD

Parental  VDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELP
          VD.N.DIND..PNC..ALRNDSYTLH.I.P.KVDPLVS..MVEKVP....EMIGGLDKQIK.I.EVIE.P
Retrocopy VDRNSDINDMRPNCQGALRNDSYTLHNIIPSKVDPLVSPVMVEKVPTLI*EMIGGLDKQIKDITEVIEPP

Parental  VKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMA
          VKHP.LFEALGI.QP..V.LYGP.GTGKT..A.AVAHHTDCTF....GSELV.KFI.EG.RMVRELFVMA
Retrocopy VKHPNLFEALGITQPRVVPLYGPLGTGKTPFA*AVAHHTDCTFVHIPGSELV*KFIREGPRMVRELFVMA

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_1480 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480 ,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,