RetrogeneDB ID: retro_nleu_2580

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397375.1:4772131..4772962(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000011873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSNLEG00000011713
• Aliases: None
• Description: None

Sequence

>retro_nleu_2580
AGGTCGCTCAAGCCCTCAGACCCTCTGAGAAAAAGCCCAACCATGGAACAAGCAGTGCAGACCGCCTCGGCCCACTTACC
TGCTCCAGCAGCTGTTGGGAGAAGGAGTCCTGTATCAACCAGGCCTTTGCCATCTACCAGCCAAAAGGCAGGAGAGAATC
AGGAGCACAGGCAAGCTGAAGTACACAAAGTTTCAAGGCCAGAAAATGAGTAACTCAGAAATGGTAACAAGAGACAAGTA
GCTCCAGGTGCTCCTTCAGCTCCAAGGAGAGGGCGTGGGGGTCATCGGAGTGGTAGGGGAAGGTTTGGTATTCGGCGAGA
TGGGCCAATGAAATCTGAGAAAGACTTTGACTTTGAAAGTGCAAATGCACAATTCCACAGGGAAGAGATTGACAGAGAGT
TTCATAATAAACTTAAATTAAAAGAAGATAAACTTGAGAAACAGGAGAAGCCTGTAAATGGTGAAGATAAAGGAGACTCA
GGAGTTGATACCCAAAACAGTGAAGGAAATGCTGATGAAGAAGATCCACTTGGACCTAATTGCTATTATGACAAAACTAA
ATCCTTCTTTGATAATATTTCTTGTGATGACAATAGAGAACGGAGACCAGCCTGGGCTAAAGAAAGAAGATTAAATGCTG
AAACATTTGGAATCCCACTTCATCCAAACTGTGGCTGTGGGGGATACAGAGGCAGAGGAGGTCTTGGTTTCCGTGGTGGC
AGAGGGTGTGGTGGTGGCAGAGGTGGTACCTTCACTGCCCCTCGAGGATTTCGCGGTGGATTCAGAGGAGGTCGTGGGAG
CTGGGAGTTTGCAGATTTTGAATATAGGAAA

Alignment

ORF - retro_nleu_2580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 59.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSSPQLNPLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLPSTSQKAGENQEHRRAEVHKVSRPENE
          RS.....PLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLPSTSQKAGENQEHR.AEVHKVSRPENE
Retrocopy RSLKPSDPLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLPSTSQKAGENQEHRQAEVHKVSRPENE

Parental  QLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKL
          .LRN.NKRQVAPGAPSAPRRGRGGHR.GRGRFGIRRDGPMK.EKDFDFESANAQF..EEIDREFHNKLKL
Retrocopy *LRNGNKRQVAPGAPSAPRRGRGGHRSGRGRFGIRRDGPMKSEKDFDFESANAQFHREEIDREFHNKLKL

Parental  KEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERR
          KEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRP.WA.ERR
Retrocopy KEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPAWAKERR

Parental  LNAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRGGGRGGTFTAPRGFRGGFRGGRGGREFADFEYRK
          LNAETFGIPL.PN.G.GGYRGRGGLGFRGGRG.GGGRGGTFTAPRGFRGGFRGGRG..EFADFEYRK
Retrocopy LNAETFGIPLHPNCGCGGYRGRGGLGFRGGRGCGGGRGGTFTAPRGFRGGFRGGRGSWEFADFEYRK

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_2580 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580 , retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,