RetrogeneDB ID: retro_sscr_641

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:124460435..124461077(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK3
• Ensembl ID: ENSSSCG00000023595
• Aliases: AK3, AK3L1
• Description: adenylate kinase 3 [Source:HGNC Symbol;Acc:17376]

Sequence

>retro_sscr_641
TCTGTGATCTTAGGCGCCCCTGGTTCAGGCAAGTGCACCCTGGCATTGCGCATCATCAAAAACTTCCAGCTGAAGAAGTT
CTCCAGCAGGGAACTGCTCCGAGACAACATGCTGAGGGATACAGAAATTGGTGTGCTGACCAAAGTTTTCATGGACCAGG
GGAAGATCATCCCCGCTGACCTCATAATTCAGTTGCTCCTCCAAGAGCTGAAAATTTTCACCTAGTATAGCTGGCTGTTG
TGTGGTTTCCCCAGGACGCTTCCACAGGCTGAAGCTCTGGATAGAGTTTATCAGATACACCTGGTGATGAACCCGAACGT
GCCCTCTGAGGTCATCTAGCAATGCCTCACTGCTCGCTGGATTCATCAAGCCAGTGGCCGCTTCTACAACCTGGAATTTA
ACCCTCCCAAAACGACTGGTGTGAACAATGTGACAGGAGAGCCTTTCATTAAGCATGTGGATGATAAACCAGAGACACTT
ATCAAAAGATTGAAGGCCTACGAAGACCAAACAAAACCGGTCCTGGATTATTACCAGAAAAAGGGAGCATTAGAAACATT
TTCTGGAACAGACACCAAAAAGATCTGGCCCTATATATGTGCTCTCCTGGAAACAAAATTGCCACAGATACACCACAAAA
GT

Alignment

ORF - retro_sscr_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.82 %
• Parental protein coverage: 94.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDDVMTRLVLHEL
          ..I.GAPGSGK.T...RI.K.F.LK..SS..LLRDNMLR.TEIGVL.K.F.DQGK.IP.D....L.L.EL
Retrocopy SVILGAPGSGKCTLALRIIKNFQLKKFSSRELLRDNMLRDTEIGVLTKVFMDQGKIIPADLIIQLLLQEL

Parental  KNLTQYSWLLDGFPRTLLQAEALDRVYQLDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTVG
          K..T.YSWLL.GFPRTL.QAEALDRVYQ...V.N.NVP.EVI.Q.LTARWIH..SGR.YN.EFNPPKT.G
Retrocopy KIFT*YSWLLCGFPRTLPQAEALDRVYQIHLVMNPNVPSEVI*QCLTARWIHQASGRFYNLEFNPPKTTG

Parental  IDDITGEPLVQREDDKPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHVYAFLQTKVPQI
          ....TGEP.....DDKPET..KRLKAYE.QT.PVL.YY.KKG.LETFSGT.T.KIWP...A.L.TK.PQI
Retrocopy VNNVTGEPFIKHVDDKPETLIKRLKAYEDQTKPVLDYYQKKGALETFSGTDTKKIWPYICALLETKLPQI

Parental  NQKT
          ..K.
Retrocopy HHKS

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	9.69 RPM
SRP014902_testis	0.00 RPM	24.75 RPM
SRP018288_heart	0.00 RPM	94.19 RPM
SRP018288_kidney	0.00 RPM	207.26 RPM
SRP018288_liver	0.00 RPM	173.18 RPM
SRP018288_lung	0.00 RPM	60.99 RPM
SRP018856_adipose	0.00 RPM	23.58 RPM
SRP035408_brain	0.00 RPM	56.41 RPM
SRP035408_liver	0.00 RPM	135.89 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_641 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323,
Callithrix jacchus	ENSCJAG00000011188	1 retrocopy	retro_cjac_1940,
Equus caballus	ENSECAG00000011235	2 retrocopies	retro_ecab_317, retro_ecab_914,
Echinops telfairi	ENSETEG00000000829	1 retrocopy	retro_etel_57,
Felis catus	ENSFCAG00000028063	2 retrocopies	retro_fcat_162, retro_fcat_1982,
Homo sapiens	ENSG00000147853	3 retrocopies	retro_hsap_1163, retro_hsap_3228, retro_hsap_555,
Gorilla gorilla	ENSGGOG00000028122	3 retrocopies	retro_ggor_2195, retro_ggor_503, retro_ggor_908,
Loxodonta africana	ENSLAFG00000001126	1 retrocopy	retro_lafr_205,
Microcebus murinus	ENSMICG00000013112	3 retrocopies	retro_mmur_1474, retro_mmur_1559, retro_mmur_1579,
Myotis lucifugus	ENSMLUG00000017272	1 retrocopy	retro_mluc_535,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Mustela putorius furo	ENSMPUG00000005006	2 retrocopies	retro_mputfur_1163, retro_mputfur_890,
Nomascus leucogenys	ENSNLEG00000008885	3 retrocopies	retro_nleu_2638, retro_nleu_2653, retro_nleu_948,
Oryctolagus cuniculus	ENSOCUG00000011411	1 retrocopy	retro_ocun_716,
Otolemur garnettii	ENSOGAG00000007477	2 retrocopies	retro_ogar_3482, retro_ogar_3492,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416, retro_ptro_796,
Pteropus vampyrus	ENSPVAG00000015751	1 retrocopy	retro_pvam_269,
Sus scrofa	ENSSSCG00000023595	1 retrocopy	retro_sscr_641 ,
Ictidomys tridecemlineatus	ENSSTOG00000000021	1 retrocopy	retro_itri_933,
Tupaia belangeri	ENSTBEG00000008054	3 retrocopies	retro_tbel_1463, retro_tbel_3247, retro_tbel_3397,
Tursiops truncatus	ENSTTRG00000016524	1 retrocopy	retro_ttru_1036,
Vicugna pacos	ENSVPAG00000009187	1 retrocopy	retro_vpac_137,