RetrogeneDB ID: retro_sscr_453

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:131846710..131847970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSSSCG00000000405
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:F1SLA0]

Sequence

>retro_sscr_453
CGATTGCCATCCACGGATGGTACAGAAGACTTTGTTAGAGGACAGAAAGTCCTGGATTCTGGTGCACCAGTCAAAATTCC
TGTTGGGCCTGAGACCTTGGGAAGAATCATGAATGTCACTGGAGAACCTATTGATGAGCGAGGTCCCATCAAAACCAAAC
AATTTGCTGCTATTTATGCTGAGGCTCTTGAATTCATGGAGATGAATGTTGAGCAGGAAATTCTGATTACTGGTATCAAG
GTTGTGGACCTACTGGCTCCTTATGCCAAGGGTGGCAAAATTGGGCTCTTTGCTGGTGCTGGAGTTGGCAAGGCAGTACT
GATGATGGAGCTAATCAACAACATAGTCAAAGCTCATGGTGGTTACTCAGTGGTTGCTGGTGTTGGTGAGAGGACCAGTG
AGGGCAATGACTTATACCATGAAATGATCGAGTCTGGTGTTATCAACTTAAAAGATGCTACCTCCAAGGTAGCACTGGTG
TATGGTCAAACAAATGAAATGCCTGGTGCTCAGTCTTTGGTAGCTCGGAGTTCACTGACTGTAGCTGAATACTTCAGAGA
TGAAGAAGATCAAGATGTACTGCTGTTTTTTGATAAGTTCTTTTGCTTCACCCAGGCTGGCTCAGAGGTGTCTGTTTTAT
TGGGCAGAATCCCTTCTGCTGTGGGTTATCAGCCTACCCTGGCCGCTGACATGGGTGCCATGCAGGAAAGAATCACCACC
ACCGGAAAAGGATCTATCACGTCTGTACAGGCCATCTACGTACCTGCTGATGACTTGACTGCCCCTGCCCCTGCCACTAC
CTTTGCCCATTTGGATGCTACCACTGCGCTGTCCCATGCTATTGCTGAGCTGGGCATTTATCTTGCTGTGGATCCTCTGG
ACTTCACTTCTCGCATCATGGATCCCAACATTGTTGGCAGTGAGCATTGTGATGTTGCCCGTGGAGTGGAAAAGATGCTA
CAGGACGACAAATCCCTCCAGGATATCATTGCCATCCTGAGTGTGAATGAACTTTCTGAGGAAGACAAGTTAACTGTGTT
CCGTGCACGGAAAATACGGCATTTCTTGTCTCAGCCATTCCAGGTTGCCGAGGTCTTTACAGATCATATGGGGAAGCTGG
TACCCCTGAAGGAGACCATCAAAGGATTCCAGCAGATTTTGGCAGCTGAATATGACCATCTCCCTTAACAGGCTTTCTAT
ATGGTGGGACCCATTGAAGAAGCTGTGGCAAAAGCTGATAAGCGGGCTGAAGAGCACTCG

Alignment

ORF - retro_sscr_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 79.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFMEMSV
          R....DGTE..VRGQKVLDSGAP.KIPVGPETLGRIMNV.GEPIDERGPIKTKQFAAI.AEA.EFMEM.V
Retrocopy RLPSTDGTEDFVRGQKVLDSGAPVKIPVGPETLGRIMNVTGEPIDERGPIKTKQFAAIYAEALEFMEMNV

Parental  EQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYH
          EQEIL.TGIKVVDLLAPYAKGGKIGLF.GAGVGK.VL.MELINN..KAHGGYSV.AGVGERT.EGNDLYH
Retrocopy EQEILITGIKVVDLLAPYAKGGKIGLFAGAGVGKAVLMMELINNIVKAHGGYSVVAGVGERTSEGNDLYH

Parental  EMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEV
          EMIESGVINLKDATSKVALVYGQ.NE.PGA...VA...LTVAEYFRD.E.QDVLLF.D..F.FTQAGSEV
Retrocopy EMIESGVINLKDATSKVALVYGQTNEMPGAQSLVARSSLTVAEYFRDEEDQDVLLFFDKFFCFTQAGSEV

Parental  SALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRA
          S.LLGRIPSAVGYQPTLA.DMG.MQERITTT.KGSITSVQAIYVPADDLT.PAPATTFAHLDATT.LS.A
Retrocopy SVLLGRIPSAVGYQPTLAADMGAMQERITTTGKGSITSVQAIYVPADDLTAPAPATTFAHLDATTALSHA

Parental  IAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRAR
          IAELGIY.AVDPLD.TSRIMDPNIVGSEH.DVARGV.K.LQD.KSLQDIIAIL...ELSEEDKLTV.RAR
Retrocopy IAELGIYLAVDPLDFTSRIMDPNIVGSEHCDVARGVEKMLQDDKSLQDIIAILSVNELSEEDKLTVFRAR

Parental  KIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS
          KI..FLSQPFQVAEVFT.H.GKLVPLKETIKGFQQILA.EYDHLP.QAFYMVGPIEEAVAKADK.AEEHS
Retrocopy KIRHFLSQPFQVAEVFTDHMGKLVPLKETIKGFQQILAAEYDHLP*QAFYMVGPIEEAVAKADKRAEEHS

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
SRP014902_placenta	0.00 RPM	326.78 RPM
SRP014902_testis	0.00 RPM	408.64 RPM
SRP018288_heart	0.10 RPM	2124.72 RPM
SRP018288_kidney	0.30 RPM	1484.87 RPM
SRP018288_liver	0.16 RPM	565.92 RPM
SRP018288_lung	0.71 RPM	153.35 RPM
SRP018856_adipose	0.00 RPM	609.27 RPM
SRP035408_brain	0.03 RPM	403.61 RPM
SRP035408_liver	0.00 RPM	412.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_453 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 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 ,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,