RetrogeneDB ID: retro_sscr_355

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:192326969..192327520(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000021535
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_355
GGGGAATGCTCAGACTGTGTGGTAAGGAGGGACCCAAACATCAAGCGCCCCAGAGGCTTCGGGTTTGTCACGTATGCCAT
TGTGGAGGAGGTGGATGCAGCCATGAATGCAAGCTGCACAAGTTGGATGGAAGAGTTGTGGAACCAAAGAGGGTCTTCTC
AAGAGAAGATTCTCAAAGACCTGGTGCCCACTTAACTGTGAAAAAGATTTTTGTGGGTGGCATTAAAGAAGACACTCAAG
AACATCACCTAAGAGAGTATTTTGAAGAGTATGGGAAAATTGAAGTGACTGAAATCATGACTGACCGAGGCAGTGGCAGA
AAGAGAGGTTTTGCTTTTGTAACCTTTGATGACCATGACTCTGCAGACAAGACTGTCGTTCAGAAATACCACACTATGAC
TGGCCAAAACTGTGAAGTGAGGAGAGCCCTATCCAAGCAAAAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTCAAAGTG
GTTCTGGAAACTTTGGTGGTGGTCAAGGAGGTGGTTTTGGTGGAAATGACAACTTTGGTTGTGGGGGAAAC

Alignment

ORF - retro_sscr_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.32 %
• Parental protein coverage: 57.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK
          G...DCVV.RDPN.KR.RGFGFVTYA.VEEVDAAMNA...HK.DGRVVEPKR..SREDSQRPGAHLTVKK
Retrocopy GECSDCVVRRDPNIKRPRGFGFVTYAIVEEVDAAMNA<KLHKLDGRVVEPKRVFSREDSQRPGAHLTVKK

Parental  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE
          IFVGGIKEDT.EHHLR.YFE.YGKIEV.EIMTDRGSG.KRGFAFVTFDDHDS.DK.V.QKYHT..G.NCE
Retrocopy IFVGGIKEDTQEHHLREYFEEYGKIEVTEIMTDRGSGRKRGFAFVTFDDHDSADKTVVQKYHTMTGQNCE

Parental  VRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGN
          VR.ALSKQ.MASASSSQRG.SGSGNFGGG.GGGFGGNDNFG.GGN
Retrocopy VRRALSKQKMASASSSQRGQSGSGNFGGGQGGGFGGNDNFGCGGN

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	0.00 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	0.00 RPM	287.36 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_355 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_355 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,