RetrogeneDB ID: retro_sscr_664

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:52610480..52610780(-)
• Located in intron of: ENSSSCG00000028260

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000024330
• Aliases: None
• Description: None

Sequence

>retro_sscr_664
ATGAACTTAGAGCAGGTGTCCAAAGGGAGAAGTTGAACCTCTGTCAAATCACCACCCGGGTAGGTTTGCTTTCCTACCTT
TTCTCTGGTTGCTCAACATCTTCTGCTTCTTCTGAGAGGCGTTCCTTGTCCCAGCACATATGGAACAGAGACAAATCAAA
GACTACGTCTGGCACTCAGCTATGTGCTTCTGCTTTTCAGGAATCATACTCAACACCTGCATCACTGTCTTCCAGATCTA
CCGGCCATGTTGGGGCACCCTTGGGGATTACCTCTCCTTCACATTTCACTGGGTACCCCC

Alignment

ORF - retro_sscr_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNLERVSN-EEKLNLCR-KYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRSAVGFLFWV
          MNLE.VS...EKLNLC......G.FAFLPFLWL.NIF.FF.EAFLVPA..EQ.QIK.YVW.SA..F.F..
Retrocopy MNLEQVSK<REKLNLCQ<NHHPGRFAFLPFLWLLNIFCFF*EAFLVPAHMEQRQIKDYVWHSAMCFCFSG

Parental  IILTTWITIFQIYRPRWGALGDYLSFT-IPLGTP
          IIL.T.IT.FQIYRP.WG.LGDYLSFT.I.LGTP
Retrocopy IILNTCITVFQIYRPCWGTLGDYLSFT<ISLGTP

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	32.25 RPM
SRP014902_testis	0.00 RPM	29.70 RPM
SRP018288_heart	0.00 RPM	16.82 RPM
SRP018288_kidney	0.00 RPM	33.10 RPM
SRP018288_liver	0.00 RPM	17.11 RPM
SRP018288_lung	0.10 RPM	39.81 RPM
SRP018856_adipose	0.00 RPM	64.30 RPM
SRP035408_brain	0.03 RPM	13.02 RPM
SRP035408_liver	0.03 RPM	8.10 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_664 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_664 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002930	1 retrocopy	retro_eeur_7,
Macropus eugenii	ENSMEUG00000012358	1 retrocopy	retro_meug_524,
Myotis lucifugus	ENSMLUG00000011528	2 retrocopies	retro_mluc_1385, retro_mluc_1860,
Mus musculus	ENSMUSG00000036835	2 retrocopies	retro_mmus_1415, retro_mmus_2454,
Sorex araneus	ENSSARG00000002056	1 retrocopy	retro_sara_708,
Sus scrofa	ENSSSCG00000024330	1 retrocopy	retro_sscr_664 ,
Tupaia belangeri	ENSTBEG00000001589	1 retrocopy	retro_tbel_447,