RetrogeneDB ID: retro_pabe_1921

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:5716337..5717337(+)
• Located in intron of: ENSPPYG00000012082

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSPPYG00000004668
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]

Sequence

>retro_pabe_1921
TCTGCTGCCTCAGCCTCAAGGGCCTTGCAGGAACTCAGCCCTTCAGTGTTGCTACCCCAAGCGCAGGTCTTGCCATGGGC
CACTCTGGCAGCAATCCAATCTACCAGGAAATATGGGCATAAACATCACCTTTGCTGAAGACAGGCACCACCACTGGGTG
TATTGTGGTGGTCATTGATGCGGTAGTGGATGTCCAGTTTGATGAGGGACTACCATCTATTCTAAATGCCCAGCAAGTAC
AAGGCAGGGAGACCAGGCTGGTTTTGGTGGTGGCCCAGCATTTGGGTGAGAGCACAGTAAGGATTACGCTATGGATGATA
CAGAAGACTTGTTTAGAGACCAGAAAGTCCTGGACTCTGGTGCACCAATCAAAAGTCCTGTTGGTCCTGAGACTTTGAGC
AGAATCATGAACATCATTGAGAGCCTACTGATGAAAGAGGTCCCATCAAAATGAAACAGTTTGCTCCCATTTATGATGAG
GCTCCTGAGTTCATGGAAATTAGTGTTGAGCAAGAAATTCTGGTGGCTAGTATCAAAGTTGTGGATCTCCTTGCTTCCTA
GCCAAGAGTGGCGAAATTGGGCTTTTTAGTGGTGTTAGAGTTGACAAGATTGTACCCATCATGGAGCTAATCAACAATGT
TGCCAGAGCCCATGGTGCTTACTCTGGGTTTGCTGGTGTTTTTGAGAGGACCTGTGAGGGCAATGACTTATATTATGAAA
TGACTGAGTCTGGTGTTGTCAACTTAAAAGATGTTACCTCCAAGGTAGTGCTGATGTACGGTCAAATGAGTGAACCACCT
GCTACTCATGCCCAGGTGTCTCTGACTGGACTGACTGTGGCTGAATACTTCAGAGACCAAGAAGTTCAAGATGTACTCCT
GTTTATTGATAATATCTTTCACTTCACCCATGCTGGCTCAAGGTGTCTGCCTTATTGGGCAGAATCCCTTCTGCTGTGGG
CTATCAGCCTTCCCTGGCCAATGACATGGTGGGTATGATG

Alignment

ORF - retro_pabe_1921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SAASASGALRELTPSASLPPGQLLLRAAPTVVHPVR-DLWRWQTSPSPKAGAPPGGIVAVIGAVVDVQFD
          SAASAS.AL.EL.PS..LP..Q.L..A........R...W...TSP..K.G...G.IV.VI.AVVDVQFD
Retrocopy SAASASRALQELSPSVLLPQAQVLPWATLAAIQSTR<EIWA*-TSPLLKTGTTTGCIVVVIDAVVDVQFD

Parental  EGLPPFLNALEVQGRETRLVLEVAQHLGESTVR-TIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIM
          EGLP..LNA..VQGRETRLVL.VAQHLGESTVR...AMD.TE.L.R.QKVLDSGAPIK.PVGPETL.RIM
Retrocopy EGLPSILNAQQVQGRETRLVLVVAQHLGESTVR<DYAMDDTEDLFRDQKVLDSGAPIKSPVGPETLSRIM

Parental  NVIG-EPIDERGPIKTKQFA-SH-SMLRAPEFMEMSVEQEF-LVTGIKVVDLLAP-YAKGGKIGLFGGAG
          N.I..EP.DERGPIK.KQFA.SH..M.R............F.LV..IKVVDLLA...AK.G.IGLF.G..
Retrocopy NIIE<EPTDERGPIKMKQFA<SH<FMMRLLSSWKLVLSKKF<LVASIKVVDLLAS<LAKSGEIGLFSGVR

Parental  VGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGAR
          V.K.V.IMELINNVA.AHG.YS.FAGV.ERT.EGNDLY.EM.ESGV.NLKD.TSKV.L.YGQM.EPP...
Retrocopy VDKIVPIMELINNVARAHGAYSGFAGVFERTCEGNDLYYEMTESGVVNLKDVTSKVVLMYGQMSEPPATH

Parental  ARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGS-EVSALLGRIPSAVGYQPTLATDMGTMM
          A.V.LTGLTVAEYFRDQE.QDVLLFIDNIF.FT.AGS..VSALLGRIPSAVGYQP.LA.DM..MM
Retrocopy AQVSLTGLTVAEYFRDQEVQDVLLFIDNIFHFTHAGS<KVSALLGRIPSAVGYQPSLANDMVGMM

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	0.00 RPM	403.12 RPM
SRP007412_cerebellum	0.00 RPM	461.35 RPM
SRP007412_heart	0.00 RPM	662.82 RPM
SRP007412_kidney	0.00 RPM	553.48 RPM
SRP007412_liver	0.00 RPM	300.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1921 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1921 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1921 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2128
Pan troglodytes	retro_ptro_1557
Gorilla gorilla	retro_ggor_1648

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921 , retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,