RetrogeneDB ID: retro_sscr_441

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:88572459..88573030(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL9
• Ensembl ID: ENSSSCG00000030373
• Aliases: None
• Description: methyltransferase like 9 [Source:HGNC Symbol;Acc:24586]

Sequence

>retro_sscr_441
GCTATGTTTGTGTTTTCACCAGATTAGTTTCAGAGACTGATTAAAATTAATCCAGACTGGAAAACCCATAGAATTCTTGC
TGGAGATGGCGAAATCACAAAAATCATGAGCTCTCATTTTGAAGAAATTTATGCCACCGAGCTGTTGGAAATGATGATAT
GGCAGCTTCAGAAGAAAAAGTACAGAGTGCTGGGTATAAATGAGTGGCAGAATACAGGGTTCCAGTATGATGTCATCAAC
TGCTCGAATTTGCTGGACCACTGTGATAGCCTCTGACTTTGCTAAAAGATATTAGAAGTGTCTTGGAGCCAAACAGAGAC
AGGGTCATCCCTGCTGTGGTGTTACCCTTTCATCTGTATGTGGAAAACATAGGTGGCCAGTGGAATAAACCCTCAGAAAT
TTTGGCACTCAAGGGACAGAATTGGGAAGAAAAGTGAATAGTCTGCCTGAAATTTTCAGAAAAGCTGGTTTGGTTATCAA
AGCGCTCACTAGACTGCCATACCTGTGCAAAGGCAACATGTATAATGACTACTATGTTTTGGATGATACTGTCTTTGTTC
TCAAACCAGTA

Alignment

ORF - retro_sscr_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 72.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGIN
          .MFVFSPD.FQRL.KINPDWKTHR.L...AGDGE.TKIMS.HFEEIYATEL.E.MIWQLQKKKYRVLGIN
Retrocopy AMFVFSPD*FQRLIKINPDWKTHRIL---AGDGEITKIMSSHFEEIYATELLEMMIWQLQKKKYRVLGIN

Parental  EWQNTGFQYDVISCLNLLDRCDQ-PLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGGKWDKPSEILE
          EWQNTGFQYDVI.C.NLLD.CD..PLTLLKDIRSVLEP.R.RVI.A.VLPFH.YVEN.GG.W.KPSEIL.
Retrocopy EWQNTGFQYDVINCSNLLDHCDS<PLTLLKDIRSVLEPNRDRVIPAVVLPFHLYVENIGGQWNKPSEILA

Parental  IKGQNWEE-QVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVFVLKPV
          .KGQNWEE..VNSLPE.FRKAG.VI.A.TRLPYLC.G.MYNDYYVLDD.VFVLKPV
Retrocopy LKGQNWEE<KVNSLPEIFRKAGLVIKALTRLPYLCKGNMYNDYYVLDDTVFVLKPV

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	29.07 RPM
SRP014902_testis	0.00 RPM	50.92 RPM
SRP018288_heart	0.00 RPM	43.56 RPM
SRP018288_kidney	0.00 RPM	54.87 RPM
SRP018288_liver	0.00 RPM	7.52 RPM
SRP018288_lung	0.00 RPM	39.30 RPM
SRP018856_adipose	0.00 RPM	36.12 RPM
SRP035408_brain	0.00 RPM	77.24 RPM
SRP035408_liver	0.00 RPM	16.59 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_441 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003533	2 retrocopies	retro_amel_402, retro_amel_704,
Canis familiaris	ENSCAFG00000017710	1 retrocopy	retro_cfam_1875,
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623,
Sus scrofa	ENSSSCG00000030373	1 retrocopy	retro_sscr_441 ,
Tupaia belangeri	ENSTBEG00000003816	2 retrocopies	retro_tbel_1726, retro_tbel_2084,
Tursiops truncatus	ENSTTRG00000015624	4 retrocopies	retro_ttru_1100, retro_ttru_1466, retro_ttru_163, retro_ttru_467,