RetrogeneDB ID: retro_sscr_313

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:23880271..23880895(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000025502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSSSCG00000006395
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_sscr_313
TCTCCACAGCCACCACCACCCTTTGGAATGGCCACCAGGGGACCTGCCTACCGTCTGGGCCGGGAGGTGCAGCAGAAGAT
TGAGAAACAATACGATGCAGATCTGGAGCAGATCCTGATCCAGTGGATCACTACCCAGTGCTGCAAGGATGTGGGCTGGC
TTCAGCCTGGGCACGAGAACTTTCAGAACTGGCTCAAAGATGGCACGGTGCTGTGTGAGCTTATTAATGGGCTGTACCCC
AAAGGGCAGGCCCCAGTGAAGAAGATCCAGGCCTCCACCATGGCCTTCAAGCAGATGGAGCAGATCTCCCCGTTCCTGCA
AGCAGCTGAGTGCTACGGCATCAACACTACTGACATCTTCCAGACTGTGGACCTCTGGGAAGGAAAGAACATGGCCTGTG
TGCAGCAGATGCTGATGAACCTGGGTGGGCTGGCGGTAGCCTGGGATTATGGGCTCTTCTCCCGGGATCCCAGTGGGTTT
CCCAAGAAATGTAAGGAAAACCCCCGGAACTTCTCTGATAACCAGCTGCAGGAGGGCAAGAATGTGATCGGGTTACAGAT
GGGGACCAACCGTGGGGCATCCTAGGCAGGCATGACCGGCTATGGGATGTCACACCAGATCCTC

Alignment

ORF - retro_sscr_313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STQPPLPFGMANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRPQPGRENFQNWLKDGTV
          S.QPP.PFGMA.RGPAY.L.REVQQKIEKQYDADLEQILIQWITTQC.KDVG..QPG.ENFQNWLKDGTV
Retrocopy SPQPPPPFGMATRGPAYRLGREVQQKIEKQYDADLEQILIQWITTQCCKDVGWLQPGHENFQNWLKDGTV

Parental  LCELINGLYPEGQAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLMN
          LCELINGLYP.GQAPVKKIQASTMAFKQMEQIS.FLQAAE.YGINTTDIFQTVDLWEGKNMACVQ..LMN
Retrocopy LCELINGLYPKGQAPVKKIQASTMAFKQMEQISPFLQAAECYGINTTDIFQTVDLWEGKNMACVQQMLMN

Parental  LGGLAVARDDGLFSGDPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMGTNRGASQAGMTGYGMPRQIL
          LGGLAVA.D.GLFS.DP..FPKK.KENPRNFSDNQLQEGKNVIGLQMGTNRGAS.AGMTGYGM..QIL
Retrocopy LGGLAVAWDYGLFSRDPSGFPKKCKENPRNFSDNQLQEGKNVIGLQMGTNRGAS*AGMTGYGMSHQIL

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	695.38 RPM
SRP014902_testis	0.14 RPM	236.22 RPM
SRP018288_heart	0.00 RPM	61.14 RPM
SRP018288_kidney	0.00 RPM	182.73 RPM
SRP018288_liver	0.00 RPM	154.47 RPM
SRP018288_lung	0.00 RPM	661.97 RPM
SRP018856_adipose	0.05 RPM	136.02 RPM
SRP035408_brain	0.00 RPM	12.89 RPM
SRP035408_liver	0.00 RPM	167.92 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_313 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_313 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313 ,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,