RetrogeneDB ID: retro_nleu_1590

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:2956567..2957498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSNLEG00000017319
• Aliases: None
• Description: None

Sequence

>retro_nleu_1590
AGCACTACAGCAGTTACTTCCTCCACAGCAACAACTGTGGCTCAGGCTCCAACCCCTGTCCTGCTTTGGCTCCCACTTTC
ACACTGCATTCATCACTCCAGTATCAGTGACAGTGTCTTCTGAACCTGCACCTGCTAGTGCAACTAAACAAGAGAAACCT
GCAGAAAAGCCAGCAGAGACACCAGTGGCTACTAGCCCGACGTCAACTGATAGTACATTGGGAGATTCTTCTTGGTCAAA
CGTTTTTGAAGATGCAACGAGTGCACTTGTGACGGGTCAGTCTTACGAGAATATGGTAACTGAGATCATGTCAATGGACT
ATGAACAAGAGCAAGTAATTGCAGCCCCAAGAGCCAGTTTCAACAACCCTGACGGGGCAGTGGAATATCTTTTAATGGGA
ATCCCTGGAGATAAAGTCAGGTTGTGATTGACCCCCACCGAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAACAGTGGCT
GCAGCTGCAGCAACTACGACAGCAACGACTACAAGTTCTGGAACATCCCCTTGAATTTTTATGGAATCAGCCTCAGTTTC
AACAGATGAGACAAATTATTCAACAGAATCCTTCCCTTCTTCCAGCGTTACTACAGTAGATATATTGAGAGAATCCTCAA
TTACTTCAGCAAATTAGCCAACACCACGAGCATTTCATTCAGATGTTAAATGAACCAGTTCGAGAAGCTGGTGGTCAAAG
AGGAGGAGATGGAGGTGGCAGTGGAGGAATTGCAGAAGCTGGAAATGGTCCTATGAACTACATTCAAGTAATGCCTCAGG
ACAAAGAAGCTATAGAAAGGTTAAAGGCATTAGGATTTCCTGAAGAACTTGTGATACAAGCATATTTTGCCTGTGAGAAG
AATAAGAATTTGGGTGCCGATTTTCTTCTACAGCAGATCTTTGATGAAGAC

Alignment

ORF - retro_nleu_1590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 77.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STTAVTSSTATTVAQAPTPV-PALAPTST-PASITPASVTASSEPAPASATKQEKPAEKPAETPVATSPT
          STTAVTSSTATTVAQAPTPV.PALAPT.T..A.ITP.SVT.SSEPAPASATKQEKPAEKPAETPVATSPT
Retrocopy STTAVTSSTATTVAQAPTPV<PALAPTFT<TAFITPVSVTVSSEPAPASATKQEKPAEKPAETPVATSPT

Parental  ATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLM-GIPG
          .TDST.GDSS.SN.FEDATSALVTGQSYENMVTEIMSM.YE.EQVIAA.RASFNNPD.AVEYLLM.G.P.
Retrocopy STDSTLGDSSWSNVFEDATSALVTGQSYENMVTEIMSMDYEQEQVIAAPRASFNNPDGAVEYLLM<GNPW

Parental  DRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGG-HPLEFLRNQPQFQQMRQIIQQNPSLLP
          .R.SQ.V.DP..AASTGAPQSS.VAAAAATTTA...TT.S.G.HPLEFL.NQPQFQQMRQIIQQNPSLLP
Retrocopy -R*SQVVIDPHRAASTGAPQSSTVAAAAATTTA---TTTSSG>HPLEFLWNQPQFQQMRQIIQQNPSLLP

Parental  ALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAI
          ALLQ.I..ENPQLLQQISQH.EHFIQMLNEPV.EAGGQ.GG.GGGSGGIAEAG.G.MNYIQV.PQ.KEAI
Retrocopy ALLQ*IY*ENPQLLQQISQHHEHFIQMLNEPVREAGGQRGGDGGGSGGIAEAGNGPMNYIQVMPQDKEAI

Parental  ERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          ERLKALGFPE.LVIQAYFACEKN.NL.A.FLLQQ.FDED
Retrocopy ERLKALGFPEELVIQAYFACEKNKNLGADFLLQQIFDED

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_1590 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590 ,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,