RetrogeneDB ID: retro_sscr_855

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:154681057..154681595(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSSSCG00000006821
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_sscr_855
GCGGCTGACCGTGGTAAAAGCCAGAGGCTGGATGTGAAATTTAGACCAGACCTGGATTTTTCTAAGCTGCCCCATCCCGT
GGACCACAAGAACGAGACTGACTCAGAGTAATGCCATCTCACTCACCCGCAGGCACAACATGTGTGGTGGGACTGAAGAG
GAAAAGATTCAAGCGGCCCTGATGGAGAACCAAATGATGCATTCTCACATGCAACTGCTAATAACTCTGCTACAACCTTG
ACCACGAGAAACAGAAGCCTTGGCCCTTGGAAGAGCTCCCCGGTCATGCTCTTTGTTTCTGGGGAAATACTCACATTTTG
CAGGAGGAAAGCTCACCTTGGTGGATTTCCTCATCGATGATGTCCTAGATCAGAACCACTTCTTTGAGCCCAAGAGCCTG
GATGGATTTTCAAATCCAAAGGCTTTCATGGGCTGTTTGGAGGCTTTGGAGAAAATAGCAGCCTACGTACGGTTGGACCG
CTTCCTCTAGATGCCCCACAAAACCAAAATGACCTGGTGAGGCAACAAAAGAGCACAC

Alignment

ORF - retro_sscr_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.68 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APDYDRSQWLDVKYKLDLDFPNLPYLMDGKN-KLTQSNAILRYIARKHNMCGETEEEKIRVDIMENQIMD
          A.D...SQ.LDVK...DLDF..LP...D.KN..LTQSNAI.....R.HNMCG.TEEEKI....MENQ.M.
Retrocopy AADRGKSQRLDVKFRPDLDFSKLPHPVDHKN>RLTQSNAIS--LTRRHNMCGGTEEEKIQAALMENQMMH

Parental  FRMQLIRLCYSPDHEKLKPQYLEQLPGQLKQFSLFLGKYSWFAGEKLTFVDFLTYDVLDQNRIFEPRCLD
          ..MQL......P.........L...P......SLFLGKYS.FAG.KLT.VDFL..DVLDQN..FEP..LD
Retrocopy SHMQLLITLLQP*PRETEALALGRAP---RSCSLFLGKYSHFAGGKLTLVDFLIDDVLDQNHFFEPKSLD

Parental  EFPNLKAFMCRFEALEKIAAYMQSDRFLKMPINNKMAQWGNKRLY
          .F.N.KAFM...EALEKIAAY...DRFL.MP...KM...GNKR..
Retrocopy GFSNPKAFMGCLEALEKIAAYVRLDRFL*MPHKTKMTW*GNKRAH

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	3.19 RPM
SRP014902_testis	0.00 RPM	22.07 RPM
SRP018288_heart	0.00 RPM	0.05 RPM
SRP018288_kidney	0.00 RPM	0.69 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	1.32 RPM
SRP018856_adipose	0.00 RPM	4.79 RPM
SRP035408_brain	0.00 RPM	12.13 RPM
SRP035408_liver	0.00 RPM	3.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_855 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_855 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855 ,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,