RetrogeneDB ID: retro_ptro_1259

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:24408136..24409616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSPTRG00000014902
• Aliases: None
• Description: None

Sequence

>retro_ptro_1259
ATGTCCGTGGACATGAATAGCCAGGGGTCTGACAGCAATGAAAAGCACTATGACTCAAATTGTGAGGAAGAGGAACAAGA
AGAGGATGAAGACCCTGGGGACATAGAGGACTATTACCTGGGAGTAGCCAGCGATGTGGAGCAGCAGGGGGCTGATGCCT
TTGGTCCTGAGGAGTACTAGTTCACTTACTTGACCTACAAGAAATCTGAGGGTGCCCTGAACGAGCACATGACCAGCTTA
GCCTCGGTCCTAAAGGTATCTCATTCAGTTGCTAAACTTATATTAGTTAATTTCCACTGGCAAGTTTCAGAGAGATTGGA
CAGATACAAGTCCAATTCTGCTCAACTGCTCGTTGAGGCTCGAGTTCAGCCTAATCCATCAAAACATGTTCCCGCATCTC
ATCCCCCTCACCACTGTGCAGTGTGTATGCAGTTTGCGTGAAAGAAAAACCTACTCTCCCTGGTCTGTCAGCACCAGTTT
TGCCGCAGCTGCTGGGAGCAGCACTGCTCAGTTCTCGTTAAGGATGGTGTGGGTGTGGGAGTCACTTGCATGGCTCAGGA
CTGTCCCACTCCATACACCAGAGGACTTTGTGTTTCAATTGCTTCCCAATGAGGAATTGAGAGAGAAATACAGGTGCTAC
CTCTTCAGGGACTATGTGAAGAGTCATTACTAGCTCCAGCTGTGCCCTGGTGCAGACTGCCTCATGGTTGTTTGGGTACA
GGAGCCTAGAGCTCACCGAGTATAGTGCAATCGGTGCAACGAGGTCTTCTGTTTCAAGTGTCATCAAATATATCACGCAC
CCACAGACCGCATCACAATCCGAAAATGGCTCACGAAGTGTGCAGACGACTCTGAAACAGCTGACTACAGTAGTGCTCAC
ACTAAAGACTGTCCCAAATACAACATCTGCATTGAGAAGAATGGAGGCTGCAATCACATGCAATGCTCCAAATGTAAACA
CGACTTCTGCTGGACATATCTAGGAGATTGGAAGGCATATGGCAGTGAATAATATGAGTGCAGTACTTACAAGGAGAATC
CTGACATTGTGAACCAGCGCCAACAAGCCCAGGCGAGGGAAGCCCTCAAGAAGTACTTATTCTACTTTGAGAGGTGGGAA
AACCACAACAAAAGCTTGCAGCTAGAGGCACAGACATACCAGCGGATTCACGAGAAGATTCAGGGGAAGGTCATGAACAA
TCTGGGGACATGGATTGACTGGCAGTACCTACAGAATGCAGCCAAGCTCTTGGCCAAGTGTTGATACACCTTGCAGTACA
TCAACCCATATACATATTACATGGAGTCTGTACCCAGGAATGAGCTGTTTGAATACCAGCAGGCTGAGCGGGAGGCTGAG
ATTGAAAACCTCTCATGGAAAGTGGAGCATGCAGACAGCTATGACAGAGGGGACTTGGAGAACCAGATGCATGTAGCCGA
GCAGTGGAGGAGAACCCTGCTGAAGGATTTCCACGATACC

Alignment

ORF - retro_ptro_1259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVDMNSQGSDSNEEDYDPNCEEEEEEEDEDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESE
          MSVDMNSQGSDSNE..YD.NCEEEE.EEDEDPGDIEDYY.GVASDVEQQGADAF.PEEY.FT.LTYK.SE
Retrocopy MSVDMNSQGSDSNEKHYDSNCEEEEQEEDEDPGDIEDYYLGVASDVEQQGADAFGPEEY*FTYLTYKKSE

Parental  GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCA
          GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSE.LDRYKSNSAQLLVEARVQPNPSKHVP.SHPPHHCA
Retrocopy GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSERLDRYKSNSAQLLVEARVQPNPSKHVPASHPPHHCA

Parental  VCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCP-LRTPEDFVFPLLPNEELREK
          VCMQF..K.NLLSL.CQHQFCRSCWEQHCSVLVKDGVGVGV.CMAQDCP.L.TPEDFVF.LLPNEELREK
Retrocopy VCMQFA*KKNLLSLVCQHQFCRSCWEQHCSVLVKDGVGVGVTCMAQDCP>LHTPEDFVFQLLPNEELREK

Parental  YRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTK
          YR.YLFRDYV.SHY.LQLCPGADC.MV..VQEPRA.RV.CNRCNEVFCFKC.Q.YHAPTD..TIRKWLTK
Retrocopy YRCYLFRDYVKSHY*LQLCPGADCLMVVWVQEPRAHRV*CNRCNEVFCFKCHQIYHAPTDRITIRKWLTK

Parental  CADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDI
          CADDSETA.Y.SAHTKDCPK.NICIEKNGGCNHMQCSKCKHDFCW..LGDWK..GSE.YECS.YKENPDI
Retrocopy CADDSETADYSSAHTKDCPKYNICIEKNGGCNHMQCSKCKHDFCWTYLGDWKAYGSE*YECSTYKENPDI

Parental  VNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAK
          VNQ.QQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQ..VMNNLGTWIDWQYLQNAAKLLAK
Retrocopy VNQRQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQGKVMNNLGTWIDWQYLQNAAKLLAK

Parental  CRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLKD
          C.YTLQY..PY.YYMES.PR..LFEYQQA..EAEIENLSWKVE.ADSYDRGDLENQMH.AEQ.RRTLLKD
Retrocopy C*YTLQYINPYTYYMESVPRNELFEYQQAEREAEIENLSWKVEHADSYDRGDLENQMHVAEQWRRTLLKD

Parental  FHDT
          FHDT
Retrocopy FHDT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	72.41 RPM
SRP007412_cerebellum	0.00 RPM	115.61 RPM
SRP007412_heart	0.12 RPM	97.06 RPM
SRP007412_kidney	0.05 RPM	88.34 RPM
SRP007412_liver	0.13 RPM	76.14 RPM
SRP007412_testis	0.00 RPM	101.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1259 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1259 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1876
Gorilla gorilla	retro_ggor_1373
Pongo abelii	retro_pabe_1557
Callithrix jacchus	retro_cjac_1106

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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,