RetrogeneDB ID: retro_sscr_1152

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:36896124..36896986(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000029660
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSSSCG00000015988
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_sscr_1152
ATGGAGGTAAAACAGCCACCCAGTCGCCCCCAGCCCAACTCCGGCAGTCACCGCCACCACCCAGATGGGGGAAAGGAGGG
CCATGATCCAAAGGAATGAGAGCAATTGAGAAAACTGTTAATTGGTGGTCTGAGCTTTGAAACTACAGATGATAGTTTAA
GAGAACATTTTGATAAATGGGGCACACTTACAGATTGTGTGGTGATGAGAGACCCCCAAACAAAACGTTCCAGGGTATTT
GGTTTTGTGACTTATTCTTGTGTTGAAGAGGTGGATGCAGAAATGTGTGCTCGACCACACAAGGTTGATGGACGTGTAGT
GGAACCAAAGAGAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTTGTTGGTG
GTAATAAAGAAGATACAGAGGAATACAATTTGAGAGACTACTTTGAAAAGTATGGCAAAATTGAAACCATAGAAGTTATG
GAAGACAGGCAGAGTGGGAAAAAGAGGATTTGCTTTTGTAACTTTCGATGATCATGATACAGTTGATAAAATTGTTGTTC
AGAAAAACCACACTATAAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAAATGCAATCTGCCAGATCA
CAGAGAGGTCGTGGAGGGGAATCTGGCAACTTTCTGGGTCATAGAGGAAACTTTGGAGGTGGTGGAGGCAACTTTGGCCA
TGGCGAAAACTTTGGTGGAAGAGGAGGTTATGGTGGTGGATGTGGTGGCAGCAGGGGTAGTTATAGAGGAGGCGATGGTG
GATATAATGGATTTGGAGGTGATGGTGGCAACTATGGTGGTGGTCCTGGTTATAGTAGTAGA

Alignment

ORF - retro_sscr_1152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.58 %
• Parental protein coverage: 75.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEVKPPPGRPQPDSGRRRRRR--GEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMR
          MEVK.PP.RPQP.SG..R.....G.EGHDPKE.EQLRKL.IGGLSFETTDDSLREHF.KWGTLTDCVVMR
Retrocopy MEVKQPPSRPQPNSGSHRHHPDGGKEGHDPKE*EQLRKLLIGGLSFETTDDSLREHFDKWGTLTDCVVMR

Parental  DPQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTE
          DPQTKRSR.FGFVTYSCVEEVDA.MCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGG.KEDTE
Retrocopy DPQTKRSRVFGFVTYSCVEEVDAEMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGNKEDTE

Parental  EYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF-DDHDTVDKIVVQKYHTINGHNCEVKKALSKQEM
          EYNLRDYFEKYGKIETIEVMEDRQSGKKR...F..F.DDHDTVDKIVVQK.HTINGHNCEVKKALSKQEM
Retrocopy EYNLRDYFEKYGKIETIEVMEDRQSGKKR-ICFCNF>DDHDTVDKIVVQKNHTINGHNCEVKKALSKQEM

Parental  QSAGSQRGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNY
          QSA.SQRGRGG.SGNF.G..GNFGGGGGNFG.G.NFGGRGGYGGG.GGSRGSY.GGDGGYNGFGGDGGNY
Retrocopy QSARSQRGRGGESGNFLGHRGNFGGGGGNFGHGENFGGRGGYGGGCGGSRGSYRGGDGGYNGFGGDGGNY

Parental  GGGPGYSSR
          GGGPGYSSR
Retrocopy GGGPGYSSR

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	0.53 RPM	49.38 RPM
SRP014902_testis	1.84 RPM	138.19 RPM
SRP018288_heart	0.29 RPM	153.18 RPM
SRP018288_kidney	0.79 RPM	270.20 RPM
SRP018288_liver	0.80 RPM	179.58 RPM
SRP018288_lung	1.53 RPM	310.16 RPM
SRP018856_adipose	9.01 RPM	442.64 RPM
SRP035408_brain	0.22 RPM	370.14 RPM
SRP035408_liver	0.09 RPM	285.07 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1152 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
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,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,