RetrogeneDB ID: retro_sscr_615

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:53419673..53420431(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSSSCG00000009988
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_sscr_615
GCATCTTCCCATAACAGACCTGGAGAAGTCAGCTGGCTAAAATCCTTGTTTGTCTGGAAGGTCAATCCAAGGAAAGATGC
TCACTCTAACCTCCTAGCCCAAAAGGAAACAAGCAGTCTGTACAAATTACAGTTTCACAATGTTAAACCAGAATACCTAA
AATCATACAACAAAATTTGTCAAGAAATGTTGCCAAAGATTCATGAAGATAAATATTACCCTTGCACTTTTGTGGGGGCT
TGGAACATGTGGTATGGTGAGCAGGATCAAGCTGTTTACCTCTGGAGCTATGAAGGAAGCTATCCAGCCCTCACAGAGGT
CATTAATAAACTTAAAGAAAATCAGCAATTTGCACAGCTCTGTAAGGCAAGAAGCAACATGCTTATCTCCGGGAAGAATC
AGCTCTTCCTGGAGCTCAGTTTCTGGAATGAGCCTGTCCCACCATTAGGACCAAGTATATATGAATTGAGATCTTACTAG
TTCCAACCAGGAACTATGATTGAATAGGGCAATTACTGGTCTTATGCTATTTACTTCAGACAAGATGGTAATGAAGCAGT
TGAAGGATTCTTCTCCCAGATTGGGCAGCTATATATGCCCATTATCTTTGGGCTTACAAGGATCTTCAGACCAGAGAAGA
TATACAGAATGCAGCATGGCATAAACATGGCTGGGAAGAACTGGTATATTATACAGTCACACTTCTTCAGGAGATGGAAT
CTGGAAGCATGATCCCACAGAAGACCTCACCCCTCCAG

Alignment

ORF - retro_sscr_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.42 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARFYSKDNEGSWFRSLFVHKVDPRKDAHSTLLSKKETSNLYKIQFHNVKPECLDAYNSLTEAVLPKLHLD
          A.......E.SW..SLFV.KV.PRKDAHS.LL..KETS.LYK.QFHNVKPE.L..YN......LPK.H.D
Retrocopy ASSHNRPGEVSWLKSLFVWKVNPRKDAHSNLLAQKETSSLYKLQFHNVKPEYLKSYNKICQEMLPKIHED

Parental  EDYPCSLVGNWNTWYGEQDQAVHLWRFSGGYPALMDCMNKLKNNKEYLEFRKERSQMLLSRRNQMLLEFS
          ..YPC..VG.WN.WYGEQDQAV.LW...G.YPAL....NKLK.N.......K.RS.ML.S..NQ..LE.S
Retrocopy KYYPCTFVGAWNMWYGEQDQAVYLWSYEGSYPALTEVINKLKENQQFAQLCKARSNMLISGKNQLFLELS

Parental  FWNEPQPRAGPNIYELRTYKLKPGTMIEWGNNWARAIKYRQENQEAVGGFFSQIGELYV-VHHLWAYKDL
          FWNEP.P..GP.IYELR.Y...PGTMIE.GN.W..AI..RQ...EAV.GFFSQIG.LY...H.LWAYKDL
Retrocopy FWNEPVPPLGPSIYELRSY*FQPGTMIE*GNYWSYAIYFRQDGNEAVEGFFSQIGQLYM<AHYLWAYKDL

Parental  QSREETRNAAWRKRGWDENVYYTVPLVRHMESRIMIPLKISPLQ
          Q.RE...NAAW.K.GW.E.VYYTV.L...MES..MIP.K.SPLQ
Retrocopy QTREDIQNAAWHKHGWEELVYYTVTLLQEMESGSMIPQKTSPLQ

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	1.19 RPM	16.33 RPM
SRP014902_testis	2.55 RPM	22.63 RPM
SRP018288_heart	0.47 RPM	2.72 RPM
SRP018288_kidney	0.59 RPM	115.15 RPM
SRP018288_liver	0.00 RPM	160.39 RPM
SRP018288_lung	0.00 RPM	9.67 RPM
SRP018856_adipose	0.06 RPM	17.97 RPM
SRP035408_brain	0.44 RPM	72.67 RPM
SRP035408_liver	0.21 RPM	196.45 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_615 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_615 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012291	1 retrocopy	retro_cfam_2091,
Otolemur garnettii	ENSOGAG00000012167	1 retrocopy	retro_ogar_2741,
Pteropus vampyrus	ENSPVAG00000017876	1 retrocopy	retro_pvam_675,
Sus scrofa	ENSSSCG00000009988	1 retrocopy	retro_sscr_615 ,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,