RetrogeneDB ID: retro_sscr_548

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:38870265..38871170(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016923
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BETA-ACTIN
• Ensembl ID: ENSSSCG00000007585
• Aliases: None
• Description: Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:Q6QAQ1]

Sequence

>retro_sscr_548
GATGATGAGCTGTCTGCCTTGGTGGTGGATAATGGCTCAGGGATGTGCAAGGCAGGCTTTGGTGGTGACGATGCCCCCCG
GGCTGTGTTCCCCTCCGTGGTAGGGCGTCCCCGGCACCAGGGCGTCATGGTAGGCATGGGCCAGAAGGACTGCTATGTGG
GGGATGAAGCCCAGAGCAAGAGGGGCATCCTGACCCTGAAGTATCCCATTGAGCATGGAGTGGTCACCAACTGGGATGAC
ATGGAGAAGATCTGGCACCACACTTTCTACAATGAGCTCCGTGTGGCACCAGATGAGCACCCCATCCTCCTCACCGAGGC
CCCCCTCAACCCCAAGATCAACCGAGAGAAAATGACTCAGATCATGTTCGAGGCTTTCAACACACCTGCCATGTATGTGG
CTATCCAGGCTGTGTTATCCCTCTATGCCTCGGGCCGGACCACTGGCATCGTGATGGATTCTGGGGATGGGGTCACTCAC
ACAGTGCCCATCTATGAAGGCTACGCCCTGCCCCATGCCATCCTCCGTCTGGACCTGGCTGGCAGAGACCTGACTGACTA
CCTCATGAAGATCCTGACGGAACGAGGCTACAACTTTACCACCACAGCCGAGCGGGAGATTGTCCGCGATGTCAAAGAGA
AGCTGTGCTACGTGGCCCTGGACTTCGAACAAGAGATGGTCGGTGCTGCTGCATCCCCCTCACTCGAAAGAAGCTATGAG
CTTCCCGATGGGCAGGTGATCACCATTGGGAATGAACGCTTTCGATGCCCTGAAGCCATTTTCCAGCCTTCCTTTCTGGG
CATTGAGTCCAGCGGGATCCATGAGACACCCTTCACTCTATCACGAGTGTGACGTGGATATTCGCAAGGACCTGTATGCC
ACACTGTGCTGTCGGAGGCAGCACA

Alignment

ORF - retro_sscr_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 80.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          DD...ALVVDNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYPI
Retrocopy DDELSALVVDNGSGMCKAGFGGDDAPRAVFPSVVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYPI

Parental  EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
          EHG.VTNWDDMEKIWHHTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVLS
Retrocopy EHGVVTNWDDMEKIWHHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVLS

Parental  LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
          LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGY.FTTTAEREIVRD
Retrocopy LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYNFTTTAEREIVRD

Parental  IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHET-TFN
          .KEKLCYVALDFEQEM..AA.S.SLE.SYELPDGQVITIGNERFRCPEA.FQPSFLG.ES.GIHET.T..
Retrocopy VKEKLCYVALDFEQEMVGAAASPSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGIESSGIHET<TLH

Parental  SIM-KCDVDIRKDLYA-NTVLS-GGTT
          SI...CDVDIRKDLYA..TVLS.GG.T
Retrocopy SIT<ECDVDIRKDLYA<HTVLS<GGST

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	0.00 RPM	7341.89 RPM
SRP014902_testis	0.00 RPM	1929.75 RPM
SRP018288_heart	0.00 RPM	240.56 RPM
SRP018288_kidney	0.00 RPM	915.41 RPM
SRP018288_liver	0.00 RPM	436.07 RPM
SRP018288_lung	0.00 RPM	3253.85 RPM
SRP018856_adipose	0.38 RPM	2025.66 RPM
SRP035408_brain	0.00 RPM	1736.76 RPM
SRP035408_liver	0.00 RPM	619.73 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_548 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_548 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548 ,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,