RetrogeneDB ID: retro_ptro_1557

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:98398894..98399960(+)
• Located in intron of: ENSPTRG00000012263

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSPTRG00000005107
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]

Sequence

>retro_ptro_1557
ATGTCTGCTGCCTCAGCCTCCAGGGACTTGCAGGAACTCAGCCCTTCAGTGTTGCTACTCCAAGCTCAGGTCTTGCCATG
GGCCACTCTGGCAGCAATCCAATCTACCAGGAAATATGGGCACAAACATCACCTTTGCTGAAGACAGGCACCACCACTGG
GTGTATTTTGGTGGTCATTGATGCAGTAGTGGATGTCCAGTTTGATGAGGGACTACCATCTATTTTAAATGCCCAGAAAG
TACAAGGCAGGGAGACCAGGCTGGTTTTGGTGGTGACCCAGCATTTGGGTGAGAGCACAGTAAGGATTATGCTATGAATG
GTACAGAAGGCTTGTTTAGAGGCCAGAAAGTCCTGGACTCTGGTGCACCAATCAAAAGTCCTGTTGGTCCTGAGACTTTG
AGCAGAATCATGAACATCATTGGAGAGCCTATTGCTGAAAGAGGTCCCATCAAAATGAAACAGTTTGCTCCCATTTATGA
TGAGGCTCCTGAGTTCATGGAAATTAGCGTTGAGCAAGAAATTCTGGTGGCTAGTATCAAAGTTGTGGATTTCCTCGCTC
CCTAGCCAAGAGTGGCAAAATTGGGCTTTTTAGTGGTGTTGGAGTTGACAAGATTGTACCCATCATGGAATTAATCAATA
ATGTTGCCAAAGCCCATGGTGCTTAATCTGGGTTTGCTGGTGTTTTTGAGAGGACCTGTAAGGGCAATGACTTATATTAT
GAAATGACTGAGTCTGGTGTTTTCAACTTAAAAGACGTTACCTCCAAGGTAATGCTGATGTAAGGTCAAATGAATGAACC
ACCTGCTACTCATGCCCAGGTAGCTCTGACTGGACTGACTGTGGCTGAATACTTCAGAGACCAAGAAGTTCAAGATGTAC
TCCTGTTTATTGATAATATCTTTCACTTCACCCATGCTGGCTCAAGGGTGTCTGCCTTATTGGGCAGAATCCCTTCTGCT
GTGGGATATCAGCCTACCCTGGCCACTGACATGGTGGGTACGATGTGGGGAAAGAATTGCCACTACCAAGAGGAGATCTA
TCACCTCTGTACAGGCTATGTACCTG

Alignment

ORF - retro_ptro_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 67.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VAVASASGALRGLTPSASLPPAQLLLRAAPTAVHPVRDYA-AQTSPSPKAGAATGRIVAVIGAVVDVQFD
          ...ASAS..L..L.PS..L..AQ.L..A...A....R.Y..AQTSP..K.G..TG.I..VI.AVVDVQFD
Retrocopy MSAASASRDLQELSPSVLLLQAQVLPWATLAAIQSTRKYG<AQTSPLLKTGTTTGCILVVIDAVVDVQFD

Parental  EGLPPILNALEVQGRETRLVLEVAQHLGESTVRTI-AMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIM
          EGLP.ILNA..VQGRETRLVL.V.QHLGESTVR...AM.GTEGL.RGQKVLDSGAPIK.PVGPETL.RIM
Retrocopy EGLPSILNAQKVQGRETRLVLVVTQHLGESTVRIM<AMNGTEGLFRGQKVLDSGAPIKSPVGPETLSRIM

Parental  NVIGEPIDERGPIKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAP-YAKGGKIGLFGGAGVGKTV
          N.IGEPI.ERGPIK.KQFAPI..EAPEFME.SVEQEILV..IKVVD.LAP..AK.GKIGLF.G.GV.K.V
Retrocopy NIIGEPIAERGPIKMKQFAPIYDEAPEFMEISVEQEILVASIKVVDFLAP<LAKSGKIGLFSGVGVDKIV

Parental  LIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVAL
          .IMELINNVAKAHG..S.FAGV.ERT..GNDLY.EM.ESGV.NLKD.TSKV.L..GQMNEPP...A.VAL
Retrocopy PIMELINNVAKAHGA*SGFAGVFERTCKGNDLYYEMTESGVFNLKDVTSKVMLM*GQMNEPPATHAQVAL

Parental  TGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDM-GTM-QERITTTKKG
          TGLTVAEYFRDQE.QDVLLFIDNIF.FT.AGS.VSALLGRIPSAVGYQPTLATDM.GTM..ERI.TTK..
Retrocopy TGLTVAEYFRDQEVQDVLLFIDNIFHFTHAGSRVSALLGRIPSAVGYQPTLATDMVGTM>GERIATTKRR

Parental  SITSVQAIYV
          SITSVQA.Y.
Retrocopy SITSVQAMYL

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	540.47 RPM
SRP007412_cerebellum	0.00 RPM	601.54 RPM
SRP007412_heart	0.03 RPM	1438.04 RPM
SRP007412_kidney	0.00 RPM	924.33 RPM
SRP007412_liver	0.07 RPM	308.62 RPM
SRP007412_testis	0.00 RPM	492.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1557 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1557 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2128
Gorilla gorilla	retro_ggor_1648
Pongo abelii	retro_pabe_1921

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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,