RetrogeneDB ID: retro_sscr_437

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:70918488..70919375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000010221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSSSCG00000022760
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_sscr_437
ATGGAAACGGAACAACCAGAGGAAACCTTTCCCAACACTGAAACCAATGGCGAATTTGGTAAACGCCCTGCTGAAGATAT
GGAAGAAGAACAAGCTTTTAAAAGATCTAGAAACACTGATGAGATGGTTGAACTGCGCATCCTGCTTCAGAGCAAGAATG
CTGGGCAGTGATTGGGAAAGGAGGCAAGAATATTAAGGCTCTCCGTACAGACTACAATGCCAGTGTTTCAGTCCCAGACA
GCAGTGGCCCCAAGCGCATATTGAGTATCAGTGCCGATATTGAAACAATTGGAGAAATTCTGAAGAAAATCATCCCTACC
TTAGAAGAGGGCCTGCAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTGTGGAATGCTTAAA
TTACCAGCACTATAAAGGAAGCGACTTTGACTGCGAGTTGAGATTGTTGATTCATCAGAGTCTGGCAGGAGGAATTATTG
GGGTCAAAGGTGCTAAAATCAAAGAACCTCGGGAGAACACTCAGACAACAATCAAGCTTTTCCAGGAATGTTGTCCTCAG
TCCACTGACAGAGTCGTTCTCATTGGAGGAAAACCTGATAGGGATGTAGAGTGTATAAAGATCATCCTTGATCTCATATC
AGAGTTGCCCATTAAAGGACGTGCTCAGCCTTATGATCCCAATTTTTACGATGAAACGTATGATTATGGTGGCTTTACAA
TGATGTTTGATGATCGCCGTGGACGTCCTGTGGGATTTCCTATGCGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGGT
CGAGGAGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGACGATATGAGCCCTCGTCGAGGACCTCCTCCCCCTCCTCC
TGGACGA

Alignment

ORF - retro_sscr_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.33 %
• Parental protein coverage: 67.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METEQRTDNRRNLSHTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAG-AVIGKGGKNIK
          METEQ......N...TETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAG.AVIGKGGKNIK
Retrocopy METEQPEETFPN---TETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAG<AVIGKGGKNIK

Parental  ALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQ
          ALRTDYNASVSVPDSSGP.RILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQ
Retrocopy ALRTDYNASVSVPDSSGPKRILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQ

Parental  HYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPQSTDRVVLIGGKPDRVVECI
          HYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKE.RENTQTTIKLFQECCPQSTDRVVLIGGKPDR.VECI
Retrocopy HYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKEPRENTQTTIKLFQECCPQSTDRVVLIGGKPDRDVECI

Parental  KIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPS
          KIILDLISE.PIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPS
Retrocopy KIILDLISELPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPS

Parental  RRDYDDMSPRRGPPPPPPGR
          RRDYDDMSPRRGPPPPPPGR
Retrocopy RRDYDDMSPRRGPPPPPPGR

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	14.20 RPM	113.75 RPM
SRP014902_testis	22.91 RPM	261.11 RPM
SRP018288_heart	25.43 RPM	194.83 RPM
SRP018288_kidney	37.83 RPM	343.59 RPM
SRP018288_liver	29.26 RPM	256.66 RPM
SRP018288_lung	35.54 RPM	371.05 RPM
SRP018856_adipose	19.17 RPM	309.97 RPM
SRP035408_brain	48.88 RPM	219.43 RPM
SRP035408_liver	59.01 RPM	204.26 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_437 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_437 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437 ,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,