RetrogeneDB ID: retro_ggor_1373

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:25807517..25808997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSGGOG00000017134
• Aliases: None
• Description: None

Sequence

>retro_ggor_1373
ATGTCCGTGGACATGAATAGCCAGGGGTCTGACGGCAATAAAAAGCACTATGACTCAAATTGTGAGGAAGAGGAACAAGA
AGAGGATGAAGACCCTGGGGACATAGAGGACTATTACCTGGGAGTAGCCAGCGATGTGGAGCAGCAGGGGGCTGATGCCT
TTGATCCTGAGGAGTACTAGTTCACTTACTTGACCTACAAGAAATCTGAGGGTGCCCTGAACGAGCACATGACCAGCTTA
GCCTCTGTCCTAAAGGTATCTCATTCAGTTGCTAAACTTATATTAGTTAATTTCCACTGGCAAGTTTCAGAGAGATTGGA
CAGATACAAGTCCAATTCTGCTCAACTGCTCGTTGAGGCTCGAGTTCAGCCTAATCCATCAAAACATGTTCCCGCATCTC
ATCCCCCTCACCACTGTGCAGTGTGTATGCAGTTTGCGCGAAAGAAAAACCTACTCTCCCTGGTCTGTCAGCACCAGTTT
TGCCGCAGCTGCTGGGAGCAGCACTGCTCAGTTCTCGTTAAGGATGGTGTGGGTGTGGGAGTCGCTTGCATGGCTCAGGA
CTGTCCCACTCCATACACCAGAGGACTTTGTGTTTCCATTGCTTCCCAGTGAAGAATTGAGAGAGAAATACAGGTGCTAC
CTCTTCAGGGACTATGTGAAGAGTCATTACTAGCTCCAGCTGTGCCCTGGTGCAGACTGCCTCATGGTTGTTCGGGTACA
GGAGCCTAGAGCTCACCGAGTATAGTGCAATCGGTGCAACGAGGTCTTCTGTTTCAAGTGTCATCAAATATATCACGCAC
CCACAGACCGCATCACAATCTGAAAATGGCTCAAGAAGTGTGCAGACGACTCTGAAACAGCCGACTACAGTAGTGCTCAC
ACTAAAGACTGTCCCGAATACAACATCTGCATTGAGAAGAATGGAGCCTGCAATCACATGCAATGCTCCAAATGTAAACA
CGACTTCTGCTGGACATATCTAGGAGATTGGAAGGCACATGGCAGTGAATAATACGAGTGCAGTACTTACAAGGAGAATC
CTGACATTGTGAACCAGCGCCAATAAGCCCAGGCGAGGGAAGCCCTCAAGAAGTACTTATTCTACTTTGAGAGGTGGGAA
AACCACAACAAAAGCTTGCAGCTAGAGGCACAGACATACCAGCGGATTCATGAGAAGATTCAGGAGAGGGTCATGAACAA
TCTGGGGACATGGATTGACTGGCAGTACCTACAGAATGCAGCCAAGCTCTTGGCCAGGTGTTGATACACCCTGCAGTACA
TCAACCCATATACATATTACATGGAGTCTGGACCCAGGAATGAACTGTTTGAATACAAGCAGGCTGAGCAGGAGGCTGAG
ATTGAAAACCTCTCATGGAAAGTGGAGCATGCAGACAGCTATGACAGAGGGGACTTGGAGAACCAGATGCATGTAGCCGA
GTAGTGGAGGAGAACCCTGCTGAAGGATTTCCACGACACC

Alignment

ORF - retro_ggor_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVDMNSQGSDSNEEDYDPNCEEEEEEEDEDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESE
          MSVDMNSQGSD.N...YD.NCEEEE.EEDEDPGDIEDYY.GVASDVEQQGADAFDPEEY.FT.LTYK.SE
Retrocopy MSVDMNSQGSDGNKKHYDSNCEEEEQEEDEDPGDIEDYYLGVASDVEQQGADAFDPEEY*FTYLTYKKSE

Parental  GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCA
          GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSE.LDRYKSNSAQLLVEARVQPNPSKHVP.SHPPHHCA
Retrocopy GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSERLDRYKSNSAQLLVEARVQPNPSKHVPASHPPHHCA

Parental  VCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCP-LRTPEDFVFPLLPNEELREK
          VCMQF.RK.NLLSL.CQHQFCRSCWEQHCSVLVKDGVGVGV.CMAQDCP.L.TPEDFVFPLLP.EELREK
Retrocopy VCMQFARKKNLLSLVCQHQFCRSCWEQHCSVLVKDGVGVGVACMAQDCP>LHTPEDFVFPLLPSEELREK

Parental  YRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTK
          YR.YLFRDYV.SHY.LQLCPGADC.MV.RVQEPRA.RV.CNRCNEVFCFKC.Q.YHAPTD..TI.KWL.K
Retrocopy YRCYLFRDYVKSHY*LQLCPGADCLMVVRVQEPRAHRV*CNRCNEVFCFKCHQIYHAPTDRITI*KWLKK

Parental  CADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDI
          CADDSETA.Y.SAHTKDCP..NICIEKNG.CNHMQCSKCKHDFCW..LGDWK.HGSE.YECS.YKENPDI
Retrocopy CADDSETADYSSAHTKDCPEYNICIEKNGACNHMQCSKCKHDFCWTYLGDWKAHGSE*YECSTYKENPDI

Parental  VNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAK
          VNQ.Q.AQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLA.
Retrocopy VNQRQ*AQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAR

Parental  CRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLKD
          C.YTLQY..PY.YYMESGPR..LFEY.QA..EAEIENLSWKVE.ADSYDRGDLENQMH.AE..RRTLLKD
Retrocopy C*YTLQYINPYTYYMESGPRNELFEYKQAEQEAEIENLSWKVEHADSYDRGDLENQMHVAE*WRRTLLKD

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	0.05 RPM	59.13 RPM
SRP007412_cerebellum	0.00 RPM	74.46 RPM
SRP007412_heart	0.03 RPM	37.24 RPM
SRP007412_kidney	0.04 RPM	69.35 RPM
SRP007412_liver	0.03 RPM	45.21 RPM
SRP007412_testis	0.21 RPM	117.17 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1373 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1876
Pan troglodytes	retro_ptro_1259
Pongo abelii	retro_pabe_1557
Callithrix jacchus	retro_cjac_1106

---

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,