RetrogeneDB ID: retro_sscr_999

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:75131684..75132053(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000016893
• Aliases: None
• Description: None

Sequence

>retro_sscr_999
TTTTCCAGGATATCATCCAAGATCTATAGGATATTACTCCTTTTAGCTGGCATTCTGGAAGAGCATATCAAATCCAGAAA
AGCCAGGCTCTTTGTTCCTGTCCACAACAACATGCCCTCTGGAATAAACAACACAAAGAAATGGAAGATGGAGTTTGGTA
CCCAAGAAAGGCGGGAAAATCCTTTGATGGGTGACTCATGAGCAGCTGATCCCTTGTCCAACATGGTTCTAACTTTCAGT
AATAAGAAGATGCAGTTGCCTTTGCAGAAACAAAACGGATGGAGCTAAGGGAGAAAGGTTCCAAAACCCAAGTCCAAGTC
TTAGGGCGCAAACTTTTCTTGGAACAAAAGAACAAGGGTATCCACAAAA

Alignment

ORF - retro_sscr_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 94.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPNIKIEIYMDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWSSTAD
          F..I...IY.....L.G..EEHIK.RK.R.FVP..NNM.SG.NNTKKWKMEF.T.ER.ENPLMG.S..AD
Retrocopy FSRISSKIYRILLLLAGILEEHIKSRKARLFVPVHNNMPSGINNTKKWKMEFGTQERRENPLMGDS*AAD

Parental  PLSNLVLTFSTK-EDAVAFAE-KNGWSFDVEERKVPKPKSKSYGANFSWNKRTRVSTK
          PLSN.VLTFS.K.EDAVAFAE..NGWS......K.PK.K..S.GANFSWNKRTRVSTK
Retrocopy PLSNMVLTFSNK<EDAVAFAE>QNGWS*GRKVPK-PKSK--S*GANFSWNKRTRVSTK

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	6.37 RPM
SRP014902_testis	0.00 RPM	20.93 RPM
SRP018288_heart	0.00 RPM	104.41 RPM
SRP018288_kidney	0.00 RPM	51.62 RPM
SRP018288_liver	0.00 RPM	32.46 RPM
SRP018288_lung	0.00 RPM	6.72 RPM
SRP018856_adipose	0.00 RPM	21.17 RPM
SRP035408_brain	0.00 RPM	62.82 RPM
SRP035408_liver	0.00 RPM	68.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_999 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133, retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Microcebus murinus	ENSMICG00000015138	1 retrocopy	retro_mmur_355,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999 ,
Tupaia belangeri	ENSTBEG00000004605	1 retrocopy	retro_tbel_2068,