RetrogeneDB ID: retro_sscr_637

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:119901883..119902680(+)
• Located in intron of: ENSSSCG00000014196

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSSSCG00000016498
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_sscr_637
GCTGCAGCTCCCTGAACAATAGCCACAACATCAAAAGCAGGAGCAGCAGTGGTCTCCCCACCCCTATCCTTGCAGTCACC
TCCAGGGCTGAGGGGTGGGAGGAGGCTGCAGCAATGGCAGTGGCTGCAGCTGGACTAAACAAGTCACCTGCAGGTATTTC
ATACATGGGGTTTGTAAAGAAGGAGATAATCGTCGCTATTCACATGACCTCTCCGACAGTCCAGCGTGCAAGTATTTTCA
GCAAGGGTACTAAATTTATGGAGACCGCTGCAGGTATGAACATAGCAAGCCACGGAAACAGGAACAAACAACTGTACAGA
TCCAATAGAAACAACTGCAGAATCATCCCTTGCTTCCTCAAGTCTCTCAGCAGCAGTTGGACCAATTGTTGAAATGAATA
TGGGTGAAGCAGAGTCAAGAAAATCAAACTTTGCAACTGTAGGAGTAGGCTCAGAAGACTGGGTGAACACCAGTGAGTTT
GTTCCTGGGCAGCCCTACTGTAGCGGTACTGCCCCTTCCTGCACTGAAGAAACCCTGAAGGGCTCTGTGACCAAGAATGA
GTCAGAGGAAGAGCAAATGGTACTGGAAACAAAGAAGCAGCTCTGCCCCTATGCTGTGGTGGGGGAGTGCAGCTATAGGG
AGAATTGTGTGTATCTCTCTATAGAGACTCCTGTGATATGTGTGGGCTGCAGGGTCTCCATCCAGTGGATGCCACCCAGA
GATCACAGCACATCAAATCTTGCATTGAGGCCCAGGAGAAAGACATGGAGCTCTCATTTGCTGTCCAGAGCAGCAAG

Alignment

ORF - retro_sscr_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.77 %
• Parental protein coverage: 55.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATTPGAGAAAAAVAAASPTPIPAVTSPSPGAGGG-GGGSDSGGGGWTKQVTCRYFMHGVCKEGDNCRYSH
          A..P...A......AA...P.....SP.PG..GG.GG.S...G..WTKQVTCRYF.HGVCKEGDN.RYSH
Retrocopy AAAP*TIATTSKAGAAVVSPPLSLQSP-PGLRGG>GGCSNGSGCSWTKQVTCRYFIHGVCKEGDNRRYSH

Parental  DLSDSPYGVVCKYFQRGYCIYGDRCRYEHSKPLKQEETT-ATDLTAESSLAASSSLS--AVVGPIVEMNM
          DLSDSP....CKYFQ.GY.IYGDRCRYEHSKP.KQE.TT..TD...........S.S..A.VGPIVEMNM
Retrocopy DLSDSP---ACKYFQQGY*IYGDRCRYEHSKPRKQEQTT<CTDPIETTAESSLASSSLSAAVGPIVEMNM

Parental  GEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPLQSSVTKQESEKEQTAVETKKQLCPY
          GEAESR.SNFATVG.GSEDWVN..EFVPGQPYC..TAPSCTE..L..SVTK.ESE.EQ...ETKKQLCPY
Retrocopy GEAESRKSNFATVGVGSEDWVNTSEFVPGQPYCSGTAPSCTEETLKGSVTKNESEEEQMVLETKKQLCPY

Parental  AAVGECRYGENCVYLHGDPCDMC-GLQV-LHPVDAAQRSQHIKSCIEAHEKDMELSFAVQRSK
          A.VGEC.Y.ENCVYL.......C.G..V.LHPVDA.QRSQHIKSCIEA.EKDMELSFAVQ.SK
Retrocopy AVVGECSYRENCVYLSIETPVICVGCRV<LHPVDATQRSQHIKSCIEAQEKDMELSFAVQSSK

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	88.00 RPM
SRP014902_testis	0.00 RPM	117.54 RPM
SRP018288_heart	0.00 RPM	41.39 RPM
SRP018288_kidney	0.00 RPM	54.08 RPM
SRP018288_liver	0.00 RPM	31.82 RPM
SRP018288_lung	0.00 RPM	78.10 RPM
SRP018856_adipose	0.05 RPM	95.01 RPM
SRP035408_brain	0.00 RPM	97.60 RPM
SRP035408_liver	0.00 RPM	35.17 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_637 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_637 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637 ,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,