RetrogeneDB ID: retro_nleu_2888

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397465.1:131576..132375(+)
• Located in intron of: ENSNLEG00000007539

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA4
• Ensembl ID: ENSNLEG00000004030
• Aliases: None
• Description: None

Sequence

>retro_nleu_2888
CCAAGTACAATTTTTTTGCCAGGAACATCAGGGAAGGGGACCAAATGAAAGAGATCTGTCAAAGGTGACCAAATGCTCTG
TCCAAAGAAGGCAGAGTGCAGTGACAACCCAGAACCTCAGAAGACGATACCAATCCCTCCATTCCCTCTAATGTGCCAGT
GTCAATCAGATTCACTGGTACATTCTGTGGGTCTGGTGCCACCAATTAAAGCTGAGCACAGAGGCCAGAAATTAGATGCA
CATAAGGGCCTGTGTTCCTTTGCCTACCCAAATCAAAAAGATATTCCTAGCCCAGGAAAAAGAGGCCAGAATCTGGAAGA
CATTATGAAAAAAATCAAAGGTGGAAAAGGGGGAGATGTCCCTGCAAAGTTCTGAGGAGATGCATCCTCCCAGAGTGGCT
CTTCTTCCTGAGGAGGGGTTGCCTGCCCTGGTAGAGTCTGCTGCTCTCCTTGAAGGAGTTAATACGGTTGTGGTGACAAC
TTCTGCCCCAGAGGCTTCGCTGGCCTCCTGGGCCAGAATTGCAGCCAGGGCAGGGATGCCAGAGGCAGTGAATGGAATCT
CCACAAGAGTGGTGTCAAGTGGCGTGTGGTCCATGGGAGAAGTCTCCCTGCAGACACGGATGGTTGGGTTCACCTCCAGT
TTCATGCTGGACAAGCCTGGGTTCCCGAGAAGCAGGAAGGGAGAGTGAGTGCACGCACGCCTCTTGCTTCCTGCCTCCAA
TTTTCCACCCCCACACCTTGCAGACAGTATGTTGAGCCCGAAATGTGTTCATAGGAACAAGATCATCAGAAGCCTCCAG

Alignment

ORF - retro_nleu_2888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.55 %
• Parental protein coverage: 87.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PNTIALPGTSAKRTKEKMSVKGNKVLCPKKKAEHTDNPRPQKKIPIPP-LPSKLP-PVNLIHRDILRAWC
          P.TI.LPGTS.K.TK.K.SVKG...LCPKK.AE..DNP.PQK.IPIPP..PS..P..VN.IH..IL..WC
Retrocopy PSTIFLPGTSGKGTK*KRSVKGDQMLCPKK-AECSDNPEPQKTIPIPP<IPSNVP<SVNQIHWYILWVWC

Parental  QQLKLSS-KGQKLDAYKRLCAFAYPNQKDFPSTAK-EAKIRKSLQKKLKVEKGETSLQSSET-HPPEVAL
          .QLKLS...GQKLDA.K.LC.FAYPNQKD.PS..K.EA.I.K.L.KK.KVEKGE.SLQSSE..HPP.VAL
Retrocopy HQLKLST<RGQKLDAHKGLCSFAYPNQKDIPSPGK>EARIWKTL*KKSKVEKGEMSLQSSEEMHPPRVAL

Parental  PPAGGPPALEHSTALLEGVNTVVVTTSAPEALLASWARISARARTPEAV-ESPQEASGVRWCVVHGKSLP
          .P..G.PAL..S.ALLEGVNTVVVTTSAPEA.LASWARI.ARA..PEAV.E.....SGV.W.VVHG.SLP
Retrocopy LPEEGLPALVESAALLEGVNTVVVTTSAPEASLASWARIAARAGMPEAV<EWNLHKSGVKWRVVHGRSLP

Parental  ADTDGWVHLQFHAGQAWVPEKQEGRVSA-LFLLPASNFPPP-HLEDNMLCPKCVHRNKVLIKSLQ
          ADTDGWVHLQFHAGQAWVPEKQEGRVSA...LL......PP.HL.D.ML.PKCVHRNK..I.SLQ
Retrocopy ADTDGWVHLQFHAGQAWVPEKQEGRVSA>ARLLLPASNFPPPHLADSMLSPKCVHRNKI-IRSLQ

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_2888 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 20 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004020	2 retrocopies	retro_nleu_1329, retro_nleu_633,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888 , retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,