RetrogeneDB ID: retro_sscr_861

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:39293227..39293795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1
• Ensembl ID: ENSSSCG00000000288
• Aliases: HNRNPA1, HNRPA1, ROA1
• Description: Sus scrofa heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001077218]

Sequence

>retro_sscr_861
GTCGTGAGGGACCCAGATACCAAGCCTTCCAGAGGCTTTAAGTTTTGTCACGTATGCCACTGTGGAGAAGGTGGATGGGG
CCATGAATGCAAGGCCACACAAGGGGGATGAAAGAGTTGTGGAACCAAAGCAGGCTGTCTCAAGAGAAGATTCTCAGGGA
CCTGGTGCTTACTTAGCTGAGAAGATTTTTGTTGGTCGCATTGAAGAAGACACTGAAGACATCATCTAAGAGATTATTTT
GAACGGTATGGGAAAACTGAAGTGACTGAAATCATGACTGACTGAGGCAGTATCAAAAAAGAGAGGCTTTGCTTTGGTAA
CCTTTGATGAACATGACTCTGTAGACGAGATTGTCCTTCGGAAATACCTCACTGTCAATGGTCACAACTGTGAAGTAAGT
AAAGCCTTATTCAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTCTAAGTGCTTCTGGAAACTTTGGTGGTGG
TCATGCAGGTGGTTTTGGTGGAAATGACAGTTTTTGTCACAGAAGAAACTTGAGTGGTTGAGGTGGCTTTGGTGGCAGTC
ATGGTGGT

Alignment

ORF - retro_sscr_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.68 %
• Parental protein coverage: 59.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VMRDPNTKRSRGF-GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIK
          V.RDP.TK.SRGF..FVTYATVE.VD.AMNARPHK.D.RVVEPK.AVSREDSQ.PGA.L...KIFVG.I.
Retrocopy VVRDPDTKPSRGF>SFVTYATVEKVDGAMNARPHKGDERVVEPKQAVSREDSQGPGAYLA-EKIFVGRIE

Parental  EDTEE-HHLRDYFEQYGKIEVIEIMTDRGS-GKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL
          EDTE..HHLRDYFE.YGK.EV.EIMTD.GS..KKRGFA.VTFD.HDSVD.IV..KY.TVNGHNCEV.KAL
Retrocopy EDTED<HHLRDYFERYGKTEVTEIMTD*GS>SKKRGFALVTFDEHDSVDEIVLRKYLTVNGHNCEVSKAL

Parental  SKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGG
          .KQEMASASSSQRG.S.SGNFGGG..GGFGGND.F....N.SG.GGFGGS.GG
Retrocopy FKQEMASASSSQRGLSASGNFGGGHAGGFGGNDSFCHRRNLSG*GGFGGSHGG

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	0.13 RPM	131.14 RPM
SRP014902_testis	0.00 RPM	558.29 RPM
SRP018288_heart	0.00 RPM	232.78 RPM
SRP018288_kidney	0.10 RPM	264.09 RPM
SRP018288_liver	0.00 RPM	139.60 RPM
SRP018288_lung	0.00 RPM	394.98 RPM
SRP018856_adipose	0.00 RPM	544.18 RPM
SRP035408_brain	0.00 RPM	569.43 RPM
SRP035408_liver	0.06 RPM	287.36 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_861 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Sus scrofa	ENSSSCG00000000288	3 retrocopies	retro_sscr_354, retro_sscr_355, retro_sscr_861 ,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,