RetrogeneDB ID: retro_pabe_1557

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:40504182..40505143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSPPYG00000013890
• Aliases: None
• Description: ariadne homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:690]

Sequence

>retro_pabe_1557
ATGTCTGTGGACGTGAATAGCCAGGCGTCTGACAGCAATGAAGAGCACTATGACTCAAATTGTGAGGAAGAGGAAGAAGA
AGAGGATGAAGACCCTGGGGACATAGAGGACTATTACCTGGGAGTAGCCAACGATGTGGAGCAGCAGGGGGCTGATGCCT
TTGATCCTGAGGAGTACCAGTTCACTTACTTGACCTACAAGAAATCTGAGGGTGCCTTGAACTAGCACATGACCAGCTTA
GCCCCTGTCCTAAAGGTGTCTCATTCAGTTGCTGAACTTACATTAGTTAATTTCCACTGGCAAATTTCAGAGAGATTGGA
CAGATACAAGTCCAATTCTGCTCAGCTGCCCGTTGAGGCTCGAGTGCAGCCTAATCCATCAAAACATGTTCCCGCATCTC
ATCCCCCTCACCACTGTGCAGTGTGTATGCAGTTTGCATGAAAGAAAAACCTACTCTCCCTGGTCTATCAGCACCAGTTT
TGCTGCAGCTGCTGGGAGCAGCACTGCTCAGTTCTTGTTAAGGATGTTGTGGGCGTGGGAGTCTGTTGCATGGCTCAGGA
CTGTCCCACTCCATACACCAGAGGACTTTGTGTTTCCATTGCTTCCCAGTGAAGAATTGAGAGAGAAATACAGGTGCCAC
CTCTTCAGGGACTATGTGAAGAGTCATTACTAGCTCCAGCTGTGCCCTGGTGCAGACTGCCTCATGGTTGTTTGGGTACA
GGAGCCTAGAGCTCACTGAGTATAGTGCAATTGGTGCAATGAGGTCTTCTGTTTCAAGTGTCATCAAATATATCACGCAT
CCACAGACTGCGTCACAATCCGAAAATGGCTCACGAAGTGTGCAGACGACTCTGAAACAGCCGACTACATTAGTGCTCAC
ACTAAAGACTGTCCCAAATGCAACATCTGCATTGAGAAGAATGGAGGCTGCAATCACATGCAATGCTCCAAATGTAAACA
C

Alignment

ORF - retro_pabe_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 70.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVDMNSQGSDSNEEDYDPNCEEEEEEEDEDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESE
          MSVD.NSQ.SDSNEE.YD.NCEEEEEEEDEDPGDIEDYY.GVA.DVEQQGADAFDPEEYQFT.LTYK.SE
Retrocopy MSVDVNSQASDSNEEHYDSNCEEEEEEEDEDPGDIEDYYLGVANDVEQQGADAFDPEEYQFTYLTYKKSE

Parental  GALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCA
          GALN.HMTSLA.VLKVSHSVA.L.LVNFHWQ.SE.LDRYKSNSAQL.VEARVQPNPSKHVP.SHPPHHCA
Retrocopy GALN*HMTSLAPVLKVSHSVAELTLVNFHWQISERLDRYKSNSAQLPVEARVQPNPSKHVPASHPPHHCA

Parental  VCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDC-PLRTPEDFVFPLLPSEELREK
          VCMQF..K.NLLSL..QHQFC.SCWEQHCSVLVKD.VGVGV.CMAQDC.PL.TPEDFVFPLLPSEELREK
Retrocopy VCMQFA*KKNLLSLVYQHQFCCSCWEQHCSVLVKDVVGVGVCCMAQDC>PLHTPEDFVFPLLPSEELREK

Parental  YRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTK
          YR..LFRDYV.SHY.LQLCPGADC.MV..VQEPRA..V.CN.CNEVFCFKC.Q.YHA.TDC.TIRKWLTK
Retrocopy YRCHLFRDYVKSHY*LQLCPGADCLMVVWVQEPRAH*V*CNWCNEVFCFKCHQIYHASTDCVTIRKWLTK

Parental  CADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKH
          CADDSETA.YISAHTKDCPKCNICIEKNGGCNHMQCSKCKH
Retrocopy CADDSETADYISAHTKDCPKCNICIEKNGGCNHMQCSKCKH

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	0.33 RPM	18.58 RPM
SRP007412_cerebellum	0.61 RPM	25.41 RPM
SRP007412_heart	0.39 RPM	21.04 RPM
SRP007412_kidney	0.03 RPM	12.00 RPM
SRP007412_liver	0.21 RPM	11.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1557 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1557 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1876
Pan troglodytes	retro_ptro_1259
Gorilla gorilla	retro_ggor_1373
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,