RetrogeneDB ID: retro_nleu_2900

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397478.1:357356..358381(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSNLEG00000005850
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_nleu_2900
ACAAAGGATGTTCTCAAATAGCATTTTAATGATTTAAAGGGAACCCTTGAGGAGCTCCTGGATGAGTGATCGGTGACCTT
TTAGCAAGAGGTGGACATCATTGAGCAGGAGACCATTAAACCATTAGATGACTGCCAGAGGCTCATAGAACACGGAGTCA
ACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCCATGGTTGGTAGTGTAGAAGAGAATGAGAAACTGTATCGCTTT
ACCAAAAAGGTCTCACACATTCAGTTGGACAGCTTACCAGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATCTGCTCA
GTTAGATGACTCAATTCTTAGAGTAAAAGACTACATTTCTAAGCATGGAACAGTAGCATCTCTCTCACCAGTACAGATAT
AATAAGAACTGATACAGAAACCTGAAGTCATCACAGTACGATGGTGTAAGGTGGATGATGATTTTACAGCCCAAGATTAC
AGGCTCTAATTTTGTAAACGTACTTCAAATCATTATGAGGATGTACATGTAGGTTCTGAAACTCAATTCATAGTATTGCA
CATAGACTCCAATGTTGATTATCAGTTCAAAGTCTGCACCTGAGGAGATGGTCAACAGGAGTGGAGCCCTGAAGTGTCCC
CCAGATAGGTCATTTCACATTGGTGCCTCATGAGTGGACAGCTGGTTTGGTGGGGTACAGTCTGAAAATCAAAGTAATAT
TGCATTCTGGAATGATTCTCAGTCCTCAGGTGTTCTCTACTCTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACAT
TCAGAGTTGCAACTGTGGGACAGAAGAGACAGTATGGGGTGTTTGCAGAAAAACAGAATGGAAACGACTCTGTGCAGCAG
GATCAAGCTATATGTATGAGTACAAATGGTGAAGTTTTTGTTAATGGAAAAGAAATGACTAATGAGTTAACCTGTTACTT
CTGGGTCCACTGTCACATTTGACATTGAAGCTGTCACTCTAGGAACTACCAATAATAATGAAGGC

Alignment

ORF - retro_nleu_2900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.49 %
• Parental protein coverage: 92.29 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTAEDLVREGEIAMLGG
          T.DVLK.HFNDLKGTL..LLDE..VT..QEVD.IEQETIKPLDDCQ.LIEHGVNTAEDLV..GEIAM.G.
Retrocopy TKDVLK*HFNDLKGTLEELLDE*SVTF*QEVDIIEQETIKPLDDCQRLIEHGVNTAEDLV*VGEIAMVGS

Parental  VGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPPVQI-EELI
          V.EENEKL..FTKK.SHIQLDSLPEVPLLVDV.CLSAQLDDSIL..VKD.I.KHGTVAS..PVQI..ELI
Retrocopy V-EENEKLYRFTKKVSHIQLDSLPEVPLLVDVLCLSAQLDDSILR-VKDYISKHGTVASLSPVQI**ELI

Parental  EKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGDGRQEW
          .KP..I.VRWCKVDDDFTAQDYRL.F.K.TSNH.EDV.VGSET.FIVLHID.NVDYQF.VC..GDG.QEW
Retrocopy QKPEVITVRWCKVDDDFTAQDYRL*FCKRTSNHYEDVHVGSETQFIVLHIDSNVDYQFKVCT*GDGQQEW

Parental  SPW-SVPQIGHSTLVPHEWTAGFEGYSL-SSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFRVETVGQP
          SP..SVPQIGH.TLVPHEWTAG..GYSL.....NIA..NDS.SSGVLYSR.PTYFCGQTLTFRV.TVGQ.
Retrocopy SPE<SVPQIGHFTLVPHEWTAGLVGYSL<ENQSNIAFWNDSQSSGVLYSRTPTYFCGQTLTFRVATVGQ-

Parental  DRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQL-PAVTSGSTVTFDIEAVTLGTTSNNE
          ......GV.AEKQ.G.DS.Q.DQA.C.STNG.VFVNGKEMTN.L.P....GSTVTFDIEAVTLGTT.NNE
Retrocopy --KRQYGVFAEKQNGNDSVQQDQAICMSTNGEVFVNGKEMTNEL>PVTS-GSTVTFDIEAVTLGTTNNNE

Parental  G
          G
Retrocopy G

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_2900 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 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900 ,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,