RetrogeneDB ID: retro_pabe_2032

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a_random:2659032..2660104(-)
• Located in intron of: None

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_2032
GCTCCTGAGTTCATGGAAATTAGTGTTGAGCAAGAAATTCTGGTGGCTAGTATCAAAGTTGTGGATCTCCTCGCTTCCTA
GCCAAGAGTGGCGAAATTGGGCTTTTTAGTGGTGTTGGAGTTGACAAGATTGTACCCATCATGCAGCTAATCAACAATGT
TGCCAGAGCCCATGGTGCTTACTCTGGGTTTGCTGGTGTTTTTGAGAGGACCTGTGAGGGCAATGACTTATATTATGAAA
TGACTGAGTCTGGTGTTGTCAACTTAAAAGATGTTACCTCCAAGGTAGTGCTGATGTACGGTCAAATGAATGAACCACCT
GCTACTCATGCCCAGGTGTCTCTGACTGGACTGACTGTGGCTGAATACTTCAGAGACCAAGAAGTTCAAGATGTACTCCT
GTTTACTGATAATATCTTTCACTTCACCCATGCTGGCTCAAGGTGTCTGCCTTATTGGGCAGAATCCCTTCTGCTGTGGG
CTGTCAGCCTACCCTGGCCACTGACATGGTGGGTATGATGTGGGGAAAGAATTGCCACTACCAAGAGGAGATCTATCACC
TCTGTACAGGCTATGTACCTGCTGATGACTCGACTGCCTCTGCTACTTCCTTTGCTCATTTGGATGCCACCACTGTGCTG
CCCCATGCTGTCACTGAGCTGGGCATCTATCTACATGTGGATCCTCTGGACTCCATCTCTCATGTCATGGATCCCAACAT
TGTTGGCAATGAGCATTATGATGTTGCCTGTGGGGTGCAAAAGATTCTGCATGGCTACAAATCCCTCCATACATTATTGT
TGTAATCCATATTGGGTATGGATTAACTTTCTGAGGAAGACAAGTTGACTGTGTCTTGAATGTGGAAAATACAACATTTC
TTGTCTCAGCCATTCCAGCTTGCTGAGGTCATCACAGGTCATATGGGGGAAGTCAGTACTCCTGAAGGAGCCCATTAAAG
GATTCCAGCAGATTTTGGGTAGGTGAACATGACCATCTCTCAGAACGGGCCTTCAGTGATGGGAACCCATTGAGAAGCTT
GGGCAAAAGCTGATACGCTGGCCTGAGAGCAC

Alignment

ORF - retro_pabe_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 68.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  APEFMEMSVEQEFLVTGIKVVDLLAP-YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGE
          APEFME.SVEQE.LV..IKVVDLLA...AK.G.IGLF.G.GV.K.V.IM.LINNVA.AHG.YS.FAGV.E
Retrocopy APEFMEISVEQEILVASIKVVDLLAS<LAKSGEIGLFSGVGVDKIVPIMQLINNVARAHGAYSGFAGVFE

Parental  RTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNI
          RT.EGNDLY.EM.ESGV.NLKD.TSKV.L.YGQMNEPP...A.V.LTGLTVAEYFRDQE.QDVLLF.DNI
Retrocopy RTCEGNDLYYEMTESGVVNLKDVTSKVVLMYGQMNEPPATHAQVSLTGLTVAEYFRDQEVQDVLLFTDNI

Parental  FRFTQAGS-EVSALLGRIPSAVGYQPTLATDMGTMMERITTTKKGSITSVQAIYVPADDLTDPAPATTFA
          F.FT.AGS..VSALLGRIPSAVG.QPTLATDM..MM..........I......YVPADD.T..A.AT.FA
Retrocopy FHFTHAGS<KVSALLGRIPSAVGCQPTLATDMVGMMWGKNCHYQEEIYHLCTGYVPADDST--ASATSFA

Parental  HLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDII--AILGMDE
          HLDATTVL..A..ELGIY..VDPLDS.S..MDPNIVG.EHYDVA.GVQKIL..YKSL.......ILGMD.
Retrocopy HLDATTVLPHAVTELGIYLHVDPLDSISHVMDPNIVGNEHYDVACGVQKILHGYKSLHTLLL*SILGMD*

Parental  LSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHM-GKLVPLKETIKGFQQIL-AGEYDHLPEQAFYMVGPI
          LSEEDKLTVS...KIQ.FLSQPFQ.AEV.TGHM.GK.V.LKE.IKGFQQIL..GE.DHL.E.AF....P.
Retrocopy LSEEDKLTVS*MWKIQHFLSQPFQLAEVITGHM>GKSVLLKEPIKGFQQIL>VGEHDHLSERAFSDGNPL

Parental  EEAVAKA-DKLAEEH
          .....K..D.LA.EH
Retrocopy -RSLGKS>DTLA*EH

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_2032 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2032 has 0 orthologous retrocopies within eutheria group .

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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,