RetrogeneDB ID: retro_sscr_625

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:70571091..70571867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSSSCG00000002023
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_sscr_625
GGAGTGGGGGATGCAGGGGACTGCGTGAACAGTTTGCAGTCTGAGGAGCTGCTGCTGGAGCCCAAGCCAGAGCCTGAGCC
TGAAGAGGAGCTGCCCCAGCCCCCCGCCCCCCATGCCACAGCTCTGGGCTCTGGGCCTGGCTTGGGAGCCCCGAGCCACC
AGGAGGAGGAGGAGCCGGGAATGGTGGAGGGTGGCCTGGGAGATGGCGCCATTAAGGACCCGGAGATGGAAGCCATCAAA
GTTGGGGAGATGGAGAAAGAAGCTGAGAAGCTAAGGGAGCTACAGAATGAAGTAAAGTAGCAGATGAATATGAATCCACC
TCCCCGCAATACTGGCCCAGGTATCGTGTCCACTGAGAAGACGGAAGCTGACACCCGCTCTATCTATGTTGGCAATGTGG
ACTCTGGTGCAACAGCAGAAGAGCTGGAAGCACACTTTCATGGCTGTGGTTCAGTCAACCACAATACTATACTTTGTGAC
AAATTTAGTGGCCATCCCAAAGGGTTTGCATATATAGAGTTCTCAGAAAAAGGGTCGGTGAGGACTTCCCTGGCCTTACA
CGAGTCCCTATTTAGAGGAAGACAAATCAAGGTGATCCCAAAAGGAACAAACAGACTGGGCATCAGCACGACAGACCAGG
GTTTTCCACGAGCTTGATACCATGCCCAGACCACCAACTATGACAGTTCCTGCTCTCGAATCTACAGTGGTTTTAACTGC
AGGCCAAGGGTCACGTCTACAGGGGCTGAGCTAGAGTGACATCATGGTATTCCCCT

Alignment

ORF - retro_sscr_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 86.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAGDYGNGLESEELEPEELLLEPEPEPEPE-EEPPRPRAPPGAPGPGPGSGAPGSQEEEEEPGLVEGDPG
          G.GD.G....S..L..EELLLEP.PEPEPE.E..........A.G.GPG.GAP.S..EEEEPG.VEG..G
Retrocopy GVGDAGDCVNS--LQSEELLLEPKPEPEPEEEXXXXXXXXATALGSGPGLGAP-SHQEEEEPGMVEGGLG

Parental  DGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADARSIYVGNVD
          DGAI.DPE.EAIK..V.EME.EAEKL.ELQNEV..QMNM.PPP.N.GP.I.S.E.K.EAD.RSIYVGNVD
Retrocopy DGAIKDPEMEAIK--VGEMEKEAEKLRELQNEVK*QMNMNPPPRNTGPGIVSTE-KTEADTRSIYVGNVD

Parental  YGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN
          .GATAEELEAHFHGCGSVN..TILCDKFSGHPKGFAYIEFS.K.SVRTSLAL.ESLFRGRQIKVIPK.TN
Retrocopy SGATAEELEAHFHGCGSVNHNTILCDKFSGHPKGFAYIEFSEKGSVRTSLALHESLFRGRQIKVIPKGTN

Parental  RPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPR-GRVYRGRARATSWYSP
          R.GISTTD.GFPRA.Y.A.TTNY.SS.SR.YSGFN.RPR.G.VYRG.AR.TSWYSP
Retrocopy RLGISTTDQGFPRA*YHAQTTNYDSSCSRIYSGFNCRPR<GHVYRG*ARVTSWYSP

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	33.05 RPM
SRP014902_testis	0.14 RPM	161.96 RPM
SRP018288_heart	0.03 RPM	51.16 RPM
SRP018288_kidney	0.00 RPM	149.73 RPM
SRP018288_liver	0.00 RPM	89.07 RPM
SRP018288_lung	0.00 RPM	91.75 RPM
SRP018856_adipose	0.15 RPM	85.98 RPM
SRP035408_brain	0.13 RPM	249.07 RPM
SRP035408_liver	0.00 RPM	122.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_625 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625 ,