RetrogeneDB ID: retro_sscr_712

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:106880345..106880754(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000008474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSSSCG00000023971
• Aliases: None
• Description: Sus scrofa H3 histone, family 3A (H3F3A), mRNA. [Source:RefSeq mRNA;Acc:NM_213930]

Sequence

>retro_sscr_712
ATGGCTCGTACAAAGCAGACCGCCCACAAATCGACTGGTGGTAAAGCACGGAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGGGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACCGTGGCACTCCGTGAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTGATTCGCAAGCTTCCCTTCCAGCGTCTTGGTGCGGGAAATTGCTCAGGACTTCAA
AACAGATATGCGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAG
ACACCAACCTGTGTGCTATCCATGCCAAACATGTAACAATTATGCCAAAAGACCTCCAGCTAGCACGCCGCATACGTGGA
GAACATGCT

Alignment

ORF - retro_sscr_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTA.KSTGGKA.RKQLATKAARK.APSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
Retrocopy MARTKQTAHKSTGGKARRKQLATKAARKGAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR

Parental  L-VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          L.VREIAQDFKTD.RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAK.VTIMPKD.QLARRIRGE.A
Retrocopy L>VREIAQDFKTDMRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKHVTIMPKDLQLARRIRGEHA

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	7.70 RPM	31.32 RPM
SRP014902_testis	3.25 RPM	34.51 RPM
SRP018288_heart	4.37 RPM	86.05 RPM
SRP018288_kidney	8.27 RPM	112.89 RPM
SRP018288_liver	8.48 RPM	57.73 RPM
SRP018288_lung	8.76 RPM	184.51 RPM
SRP018856_adipose	0.37 RPM	67.83 RPM
SRP035408_brain	0.41 RPM	19.12 RPM
SRP035408_liver	0.62 RPM	24.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_712 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_712 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macropus eugenii	ENSMEUG00000004090	5 retrocopies	retro_meug_1041, retro_meug_1065, retro_meug_1819, retro_meug_281, retro_meug_573,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Oreochromis niloticus	ENSONIG00000015805	7 retrocopies	retro_onil_45, retro_onil_47, retro_onil_51, retro_onil_54, retro_onil_61, retro_onil_65, retro_onil_69,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Sus scrofa	ENSSSCG00000023971	2 retrocopies	retro_sscr_31, retro_sscr_712 ,