RetrogeneDB ID: retro_pabe_389

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:53217929..53218954(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6AP2
• Ensembl ID: ENSPPYG00000020251
• Aliases: ATP6AP2, ATP6IP2
• Description: Renin receptor [Source:UniProtKB/Swiss-Prot;Acc:Q5R563]

Sequence

>retro_pabe_389
GTGTTTGCCGTGCTCCTGTCGTTGGTGGCGGGTGTTTGAGGAAACGAGTTTAGTTCTTGGTCTGTTATTTTCAGAAATGG
AAATTGGCCTATACCAGGAGAGTGAATCCCGGACGTGGCTGCATTGTCCATGGCCTTCTCTGTGAAGGAAAACCTTTCTT
GGCCAGGACTTGCAGTAGGTGACCGATTTCATCGTCCTTGGGCCACCGTCGTGGTGATGGTGAAGGGAGTGGACAAACTG
GCTCTACCACCAGGCAGTGTCATTTCATACCCTTTGAAGAATGCAGTTCCTTTTGGTCTTGACAGTGTTGCAAATTCCAT
TCGCTCTTTATTTTCTGAGGAAACTCCTGTTGTTTTGCAGTTGGCTCCTAGTGAGGAAAGAGCATATTTGGTAGGGAAGG
CAAACTCAGTGTTTGAAGACCTTTCAGTCACCTTAGGACAGCTCCATAATTACTTGTTTCAGGAAAACTCCATTCTCAGT
TCACTTCCCCTGAATTCTCTGAGTAGGAACAATGGAGTTGACCTGCTCTTTCTTTCTGAACTCCAAGTGCTACATGATAT
TTCAAGCTTGGTGTCTTGTCATAAGCATCTAGCCAAGGATCATTCTCCTGATTTATATTCAGTGGAGCTGGCAGGTTTGG
CTGAAATTGGGAAGCATTACGGGGAAGACTCTGAACAATTCAGAGTTGCTTCTAAAATCCTGTTGACGCTCTGCAAAAGT
TTGCAGATAACATGTACAATCTTTACAGTGGGAATGCAGTGGTAGAGTTAGTCACTATTAAGTCATTTGACACCTCCCTT
ATGAGGAAGGCAAGGACTATCTTTGAGGCAAAATAAGTGAAGAACCCAGCAAGTCCCTATAACCTTGCGTATAATTTTGA
ATATTCAGTGATTTTCAACATGATACTTTGGATAATGATTGCCTTGGCCCTGGCTGTGATTATCACTTCTTACAATATTT
GGAACATGGATCCTGGATATGATAGCATCATTTATAGGATTACGAACCAGAAGATTCGAATAGAT

Alignment

ORF - retro_pabe_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRP
          VF.VLL.LVAGV.GNEF....S..SV.FRNGNWPIPGE.IPDVAALSM.FSVKE.LSWPGLAVG..FHRP
Retrocopy VFAVLLSLVAGV*GNEF----SSWSVIFRNGNWPIPGE*IPDVAALSMAFSVKENLSWPGLAVGDRFHRP

Parental  RATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANS
          .ATV.VMVKGV.KLALPPGSVISYPL.NAVPF.LDSVANSI.SLFSEETPVVLQLAPSEER.Y.VGKANS
Retrocopy WATVVVMVKGVDKLALPPGSVISYPLKNAVPFGLDSVANSIRSLFSEETPVVLQLAPSEERAYLVGKANS

Parental  VFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLY
          VFEDLSVTL.QL.N.LFQENS.LSSLPLNSLSRNN.VDLLFLSELQVLHDISSL.S.HKHLAKDHSPDLY
Retrocopy VFEDLSVTLGQLHNYLFQENSILSSLPLNSLSRNNGVDLLFLSELQVLHDISSLVSCHKHLAKDHSPDLY

Parental  SLELAGLDEIGKRYGEDSEQFRDASKIL-VDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRTIL
          S.ELAGL.EIGK.YGEDSEQFR.ASKIL.VDALQKFAD.MY.LY.GNAVVELVT.KSFDTSL.RK.RTI.
Retrocopy SVELAGLAEIGKHYGEDSEQFRVASKIL<VDALQKFADNMYNLYSGNAVVELVTIKSFDTSLMRKARTIF

Parental  EAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD
          EAK..KNPASPYNLA..YNFEYSV.FNM.LWIMIALALAVIITSYNIWNMDPGYDSIIYR.TNQKIR.D
Retrocopy EAK*VKNPASPYNLA--YNFEYSVIFNMILWIMIALALAVIITSYNIWNMDPGYDSIIYRITNQKIRID

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	0.06 RPM	92.34 RPM
SRP007412_cerebellum	0.00 RPM	70.41 RPM
SRP007412_heart	0.03 RPM	21.25 RPM
SRP007412_kidney	0.07 RPM	113.43 RPM
SRP007412_liver	0.00 RPM	22.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_389 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_389 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_280
Pan troglodytes	retro_ptro_233
Gorilla gorilla	retro_ggor_323
Macaca mulatta	retro_mmul_561

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006109	1 retrocopy	retro_dnov_2102,
Homo sapiens	ENSG00000182220	1 retrocopy	retro_hsap_280,
Gorilla gorilla	ENSGGOG00000000532	1 retrocopy	retro_ggor_323,
Myotis lucifugus	ENSMLUG00000001159	1 retrocopy	retro_mluc_1613,
Macaca mulatta	ENSMMUG00000012762	1 retrocopy	retro_mmul_561,
Nomascus leucogenys	ENSNLEG00000001441	1 retrocopy	retro_nleu_1491,
Pongo abelii	ENSPPYG00000020251	1 retrocopy	retro_pabe_389 ,
Pan troglodytes	ENSPTRG00000021803	1 retrocopy	retro_ptro_233,