RetrogeneDB ID: retro_sscr_468

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:96464234..96464540(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000007947
• Aliases: None
• Description: None

Sequence

>retro_sscr_468
GCCAAGTACCTGGCCCAGATCACTGTGATGGGTACGTGGTTGGGCAGGGCCTTTGCTTGGGCCCTGTGGCATGAGTTTGC
AGCGAGGCAGGCAGCAGGTGATGCCCAGGTACTCACTGGACACCTGTCTACACAAGCTTCCAACCTCTCTGGCCTCAGTA
TCCTAGAGTCACAATAGATTCTCAGTGTCTCCAAACTGAGCCCCAAGGAGACCCAGAAGAACTACAAACATCTATTTAAG
GTAAACAGTAAATCTGTGGGTGGCTCCTTCTACCTGCAGTCAAAGGCAGTTAGAGCTAAGGAGCAA

Alignment

ORF - retro_sscr_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 83.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKYLAQIIVMGVQVVGRAFARALRQEFAASRAAADARGRAGHQSAAASNLSGLSLQEAQQILNVSKLSPE
          AKYLAQI.VMG....GRAFA.AL..EFAA..AA.DA....GH.S..ASNLSGLS..E.Q.IL.VSKLSP.
Retrocopy AKYLAQITVMGTWL-GRAFAWALWHEFAARQAAGDAQVLTGHLSTQASNLSGLSILESQ*ILSVSKLSPK

Parental  EIQKNYEHLFKVNDKSVGGSFYLQSKVVRAKER
          E.QKNY.HLFKVN.KSVGGSFYLQSK.VRAKE.
Retrocopy ETQKNYKHLFKVNSKSVGGSFYLQSKAVRAKEQ

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	8.49 RPM
SRP014902_testis	0.00 RPM	6.93 RPM
SRP018288_heart	0.00 RPM	17.13 RPM
SRP018288_kidney	0.00 RPM	12.61 RPM
SRP018288_liver	0.00 RPM	8.80 RPM
SRP018288_lung	0.00 RPM	9.06 RPM
SRP018856_adipose	0.00 RPM	8.69 RPM
SRP035408_brain	0.00 RPM	6.92 RPM
SRP035408_liver	0.00 RPM	5.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_468 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468 ,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,