RetrogeneDB ID: retro_nleu_450

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:43352411..43353162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000005021
• Aliases: None
• Description: None

Sequence

>retro_nleu_450
GCCATCTTCTTCAATTATATCAGTGGCATGCAGCAGGACACTATCCTGGCCAAAGGCTTCATTTCAGGATTCCCTGGTCT
CAGTACCCCATTAACAATGATATTCTGACCAGACCTTGAAAAATTTACTCCCTAACAGGCTCAAAAGACCTGCAGATGGT
GAACATATCCCTGTACATGGTGTCTCAACCCAATGTTCAGGAGCTTCCTAGCATGCACAAGCACCTAGGGCTAGACAACA
GAGAATGAGTGTTGCTATCCATTGTCAAAAGAGTACTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCACAGCTGATTACC
CAGTGGACCCAGGTATCCCTGTTGATTCAATGGGAGCTGCCAGAGAGGGCCAAGGACTTCAGTCTTATCTTGGATGATGT
AGCCATCACAGAGCTGAGCTTTAGCTGAGAGTACACAGCTACTGTAGAGGCCAAACAAGTCGTCCAGCAGGAGGTCCAGC
AGGCCCAGTTCTTGGTAGAAAAAGCAAAACTAGAACACCAGCAGAAGACTGCCCAGGCCAAGTGTGAAGCCGAGGCCGCT
AAGATGCTTGGGGAAGCACTGAGCAAGAACCCTGGCTACATCAAAACTCACAAGATTAGGCAGCCCAGAACATCTCCAAG
ACAATCACATCACAGAATCATATCTGTCTCACTGATGACAATCTTGTGCTGAACCTACAGGATAAGACTTTCACCTGGGG
AAATAAAGGCAGCCTCATTAAGGGTAAGAAA

Alignment

ORF - retro_nleu_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.02 %
• Parental protein coverage: 83.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIFFNRIGGVQQDTILAEG-LHFRIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQEL
          AIFFN.I.G.QQDTILA.G.LHFRIPW.QYPI..DI..RP.KI.S.TGSKDLQMVNISL...S.PN.QEL
Retrocopy AIFFNYISGMQQDTILAKG<LHFRIPWSQYPINNDILTRP*KIYSLTGSKDLQMVNISLYMVSQPNVQEL

Parental  PSMYQRLGLDYEERVLPSIVNEVLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITEL
          PSM...LGLD..E.VL.SIV..VLKSVVAKFNASQLITQ..QVSLLI..EL.ERAKDFSLILDDVAITEL
Retrocopy PSMHKHLGLDNRE*VLLSIVKRVLKSVVAKFNASQLITQWTQVSLLIQWELPERAKDFSLILDDVAITEL

Parental  SFSREYTAAVEAKQVAQQEAQRAQFLVEKAKQEQRQKIVQAEAQRRTGARECEALSKNPGYIKLRKIR-A
          SFS.EYTA.VEAKQV.QQE.Q.AQFLVEKAK.E..QK..QA...........EALSKNPGYIK..KIR.A
Retrocopy SFS*EYTATVEAKQVVQQEVQQAQFLVEKAKLEHQQKTAQAKCEAEAAKMLGEALSKNPGYIKTHKIR<A

Parental  AQNISKTIATSQNRIYLTADNLVLNLQDESFTRGS-DSLIKGKK
          AQNISKTI.TSQN.I.LT.DNLVLNLQD..FT.G...SLIKGKK
Retrocopy AQNISKTI-TSQNHICLTDDNLVLNLQDKTFTWGNKGSLIKGKK

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_450 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450 ,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,