RetrogeneDB ID: retro_sscr_546

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:36278930..36279386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSSSCG00000000402
• Aliases: None
• Description: RNA binding motif, single stranded interacting protein 2 [Source:HGNC Symbol;Acc:9909]

Sequence

>retro_sscr_546
ATGGCACCACCCAGTCCAAGCACAGTACCCCTAACAGCAGCAATGGGAGCAATCAATGTAAATGACCAGCTGAGTAAAAT
CAATCTCTACATCCCGGGACTGCAGCCAGGCACTACTGACCAGGACCTAGTCAAGTTGTGTCAGTCATATGGCAAGACTG
TCTCCACTAAGGCCATACTGGATAAGACCACAAACAAATGCAAAGGCTATGGCTTTGTGGACTTTGACAGTCCTTCAGCA
GCACAGAAAGCTATAACAGCACTAAAAGTCAGTGGTGTACAAGCACAGATGGCAAAGCAACAAGAGCAGGACCCCACAAA
TCTACACATATCAAACCTCCCACTGTCAATGGATGAACAAGAACTGGAGGGAATGCTGAAGCCTTTTGGCCAGATTATCT
CCACTTGAATCCTTCAAGACACCAGTGGGAACAGCAGAGGCGTTGGCTTTGCAAGG

Alignment

ORF - retro_sscr_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 53.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPSPSNSTPNSSNGS-NVNDQLSKTNLYIRGLQPGTTDQDLVKLCQSYGKIVSTKAILDKTTNKCKGY
          MAPPSPS........G..NVNDQLSK.NLYI.GLQPGTTDQDLVKLCQSYGK.VSTKAILDKTTNKCKGY
Retrocopy MAPPSPSTVPLTAAMGAINVNDQLSKINLYIPGLQPGTTDQDLVKLCQSYGKTVSTKAILDKTTNKCKGY

Parental  GFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELEGMLKPFGQVISTRILRD
          GFVDFDSPSAAQKA.TALK.SGVQAQMAKQQEQDPTNL.ISNLPLSMDEQELEGMLKPFGQ.IST.IL.D
Retrocopy GFVDFDSPSAAQKAITALKVSGVQAQMAKQQEQDPTNLHISNLPLSMDEQELEGMLKPFGQIIST*ILQD

Parental  TSGTSRGVGFAR
          TSG.SRGVGFAR
Retrocopy TSGNSRGVGFAR

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	18.45 RPM
SRP014902_testis	0.00 RPM	16.12 RPM
SRP018288_heart	0.00 RPM	16.69 RPM
SRP018288_kidney	0.00 RPM	5.81 RPM
SRP018288_liver	0.00 RPM	6.56 RPM
SRP018288_lung	0.00 RPM	53.46 RPM
SRP018856_adipose	0.00 RPM	35.89 RPM
SRP035408_brain	0.00 RPM	0.86 RPM
SRP035408_liver	0.00 RPM	5.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_546 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Myotis lucifugus	ENSMLUG00000000530	1 retrocopy	retro_mluc_1093,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546 ,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,