RetrogeneDB ID: retro_nleu_1228

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:8715442..8716921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSNLEG00000006710
• Aliases: None
• Description: None

Sequence

>retro_nleu_1228
ATGTCCGTGGAAATGAATAGCCAGGTGTCTGACAGCAGTGAAAGGCACTATGACTCAAATTGTGAGGAAGAGGAAGAAGA
AGAGGATAAAGACCCTGGGGACATAGAGGACTATTACCTGGGAGTACCCAGAGATGTGGAGCAGCAGGGGGCTGATGCCT
TTGATCCTGAGGAGTACCAGTTCACTTACCTGACCTACAAGAAATCTGAGGGTGCCCTGAATGAGCACATGACCATCTTA
GCCTCTGTCCTAAAGTTATCTCATTCAGTTGCTAAACTTATATTAGTTAATTTCCACTGGCAAGTTTCAGAGAGATTGGA
CAGATACAAGTCCAATTCTGCTCAACTGCTCATTGAGGCTCGAGTTCAGCCTAATCCATCAAAACATGTTCCCGCGTCTC
ATCCCCCTCACCACTGTGCAGTGTGTATGCAGTTTGCGGGAAAGAAAAACCTACTCTCCTTGGTCTGTCAGCACCAGTTT
TGCTGCAGCTGCTGGGAGCAGCACTGCTCAGTTCTCATTAAGGATGGTGTGGGCGTGGGAGTCTCTTGCATGGCTCAGGA
CTGTCCCACTTCATACACCAGAGGACTTTGTATATCCATTGCTTCCCAATGAAGAATTGAGAGAGAAATACAGGTGCTAC
CTCTTCAGGGACTATGTGAAGAGTCATTACTAGCTCCAGCTGTGCCCTGGTGCAGACTGCCTCATGGTTATTCGGGTACA
GGAGCCTAGAGCTCACCGCGTATAGTGCAATAGGTGCAACGAGGTCTTCTGTTTCAAGTGTCATCAAATATATCGCTCAC
CCACAGACTGCGTCACAATCCAAAAACGGCTCATGAAGTGTGCAGACGACTCTGAAACAGCTGACTACATTAGTGCTCAC
ACTAAAGACTGTCCCAAATGCAACATCTGCATTGAGAAGAATGGAGGCTGCAATCACATGCAATGCTCCAAATGTAAACA
CGACTTCTGCTGGACATATCTACGAGATTGGAAGGCACATGGCAGTGAATAATATGAGTGCAGTACTTACAAGGAGAATC
CTGACATTGTGAACCAGCGCCAACAAGCCCAGGCGAGGGAAGCCCTCAAGAAGTACTATTCTACTTTGAGAGGTGGGAAA
ACCACAACAAAAGCTTGCAGCTAGAGGCACAGACATACCAGCGGATTCACGAGAATATTCAGGAGAGGGTCATGAACAAT
CTGGGGACATGGATTGACTGGCAGTACCTACAGAATGCAGCCAAGCTCCTGGCCAAGTGTTGGTACACCCTGCAATACAT
CAACCCATATGCATATTACATGGAGTCTGGACCCAGGAAGAAGCTGTTTGAATACCAGCAGGCTGAGCGGGAGGCTGAGA
TTGAAAACCTCTCATGGAAAGTGGAGCATGCAGACTGCTATGACAGAGGGGACTTGGAGAACCAGATGCATATAACTGAG
CAGTGGAGGAGAACCCTGCTGAAGGATTTCCATGACACC

Alignment

ORF - retro_nleu_1228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVDMNSQGSDSNEEDYDPNCEEEEEEEDEDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESE
          MSV.MNSQ.SDS.E..YD.NCEEEEEEED.DPGDIEDYY.GV..DVEQQGADAFDPEEYQFT.LTYK.SE
Retrocopy MSVEMNSQVSDSSERHYDSNCEEEEEEEDKDPGDIEDYYLGVPRDVEQQGADAFDPEEYQFTYLTYKKSE

Parental  GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCA
          GALNEHMT.LASVLK.SHSVAKLILVNFHWQVSE.LDRYKSNSAQLL.EARVQPNPSKHVP.SHPPHHCA
Retrocopy GALNEHMTILASVLKLSHSVAKLILVNFHWQVSERLDRYKSNSAQLLIEARVQPNPSKHVPASHPPHHCA

Parental  VCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDC-PLRTPEDFVFPLLPNEELREK
          VCMQF..K.NLLSL.CQHQFC.SCWEQHCSVL.KDGVGVGVSCMAQDC.PL.TPEDFV.PLLPNEELREK
Retrocopy VCMQFAGKKNLLSLVCQHQFCCSCWEQHCSVLIKDGVGVGVSCMAQDC>PLHTPEDFVYPLLPNEELREK

Parental  YRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTK
          YR.YLFRDYV.SHY.LQLCPGADC.MVIRVQEPRA.RV.CNRCNEVFCFKC.Q.Y..PTDC.TI.K.L.K
Retrocopy YRCYLFRDYVKSHY*LQLCPGADCLMVIRVQEPRAHRV*CNRCNEVFCFKCHQIYRSPTDCVTIQKRLMK

Parental  CADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDI
          CADDSETA.YISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCW..L.DWK.HGSE.YECS.YKENPDI
Retrocopy CADDSETADYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWTYLRDWKAHGSE*YECSTYKENPDI

Parental  VNQSQQAQAREALKKY-LFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLA
          VNQ.QQAQAREALKKY.LFYFERWENHNKSLQLEAQTYQRIHE.IQERVMNNLGTWIDWQYLQNAAKLLA
Retrocopy VNQRQQAQAREALKKY<LFYFERWENHNKSLQLEAQTYQRIHENIQERVMNNLGTWIDWQYLQNAAKLLA

Parental  KCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLK
          KC.YTLQY..PYAYYMESGPRKKLFEYQQA..EAEIENLSWKVE.AD.YDRGDLENQMHI.EQ.RRTLLK
Retrocopy KCWYTLQYINPYAYYMESGPRKKLFEYQQAEREAEIENLSWKVEHADCYDRGDLENQMHITEQWRRTLLK

Parental  DFHDT
          DFHDT
Retrocopy DFHDT

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_1228 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013035	1 retrocopy	retro_amel_1021,
Callithrix jacchus	ENSCJAG00000003305	1 retrocopy	retro_cjac_1106,
Homo sapiens	ENSG00000177479	1 retrocopy	retro_hsap_1876,
Gorilla gorilla	ENSGGOG00000017134	1 retrocopy	retro_ggor_1373,
Myotis lucifugus	ENSMLUG00000013946	1 retrocopy	retro_mluc_1869,
Mustela putorius furo	ENSMPUG00000014344	1 retrocopy	retro_mputfur_610,
Mus musculus	ENSMUSG00000064145	1 retrocopy	retro_mmus_795,
Nomascus leucogenys	ENSNLEG00000006710	1 retrocopy	retro_nleu_1228 ,
Oryctolagus cuniculus	ENSOCUG00000017699	1 retrocopy	retro_ocun_1838,
Pongo abelii	ENSPPYG00000013890	1 retrocopy	retro_pabe_1557,
Pan troglodytes	ENSPTRG00000014902	1 retrocopy	retro_ptro_1259,
Ictidomys tridecemlineatus	ENSSTOG00000001766	1 retrocopy	retro_itri_1047,