RetrogeneDB ID: retro_sscr_820

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:57049690..57049968(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLIRP
• Ensembl ID: ENSSSCG00000028167
• Aliases: None
• Description: SRA stem-loop interacting RNA binding protein [Source:HGNC Symbol;Acc:20495]

Sequence

>retro_sscr_820
AATATCGTTGGCCCTGTTGCACTTGTCAGGAAAATTCCCTGGACCATGGTCTCAAATGTGCCGAGAGAACATTTTGAACA
ATTTGGCCATATATGAAAGTGCATGGTCCCTTTGACAAAGAGAGTGGCTTTCACAGAGGTATGGGTTGGATTCAGTTTTC
CTCAGAACTTCGCAATGTACACAACGGGAAAATCATGTATGGAGTACAGCTCCATGTTCCAGCTCAAAAATGCCAAGCTT
TCCAAGGGGAACAAACGTCTGATGAAGAGAAAGATTTT

Alignment

ORF - retro_sscr_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVGRPVAFVRKIPWTAASNELREHFAQFGHIRKCIVP-FDKETGFHRGMGWIQFSSEEELHNVLQQENHV
          N...PVA.VRKIPWT..SN..REHF.QFGHI.KC.VP.FDKE.GFHRGMGWIQFSSE..L.NV.......
Retrocopy NIVGPVALVRKIPWTMVSNVPREHFEQFGHI*KCMVP<FDKESGFHRGMGWIQFSSE--LRNV--HNGKI

Parental  IDGVKLHVQAQKRKALQGDQTSDEEKDF
          ..GV.LHV.AQK..A.QG.QTSDEEKDF
Retrocopy MYGVQLHVPAQKCQAFQGEQTSDEEKDF

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	13.80 RPM
SRP014902_testis	0.00 RPM	13.15 RPM
SRP018288_heart	0.00 RPM	19.30 RPM
SRP018288_kidney	0.00 RPM	12.51 RPM
SRP018288_liver	0.00 RPM	9.59 RPM
SRP018288_lung	0.00 RPM	2.95 RPM
SRP018856_adipose	0.00 RPM	33.43 RPM
SRP035408_brain	0.03 RPM	2.25 RPM
SRP035408_liver	0.00 RPM	2.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_820 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_820 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003975	3 retrocopies	retro_amel_307, retro_amel_326, retro_amel_340,
Bos taurus	ENSBTAG00000008135	3 retrocopies	retro_btau_1439, retro_btau_430, retro_btau_999,
Canis familiaris	ENSCAFG00000017230	1 retrocopy	retro_cfam_1303,
Callithrix jacchus	ENSCJAG00000016946	4 retrocopies	retro_cjac_1116, retro_cjac_1307, retro_cjac_3298, retro_cjac_4132,
Cavia porcellus	ENSCPOG00000001500	2 retrocopies	retro_cpor_1388, retro_cpor_579,
Dasypus novemcinctus	ENSDNOG00000007721	3 retrocopies	retro_dnov_1721, retro_dnov_2460, retro_dnov_612,
Echinops telfairi	ENSETEG00000010345	4 retrocopies	retro_etel_1095, retro_etel_1277, retro_etel_1471, retro_etel_1792,
Felis catus	ENSFCAG00000024050	2 retrocopies	retro_fcat_1696, retro_fcat_695,
Homo sapiens	ENSG00000119705	1 retrocopy	retro_hsap_4769,
Gorilla gorilla	ENSGGOG00000011059	1 retrocopy	retro_ggor_2972,
Microcebus murinus	ENSMICG00000012080	3 retrocopies	retro_mmur_1254, retro_mmur_1504, retro_mmur_238,
Macaca mulatta	ENSMMUG00000029256	1 retrocopy	retro_mmul_2544,
Mus musculus	ENSMUSG00000021040	1 retrocopy	retro_mmus_1954,
Pongo abelii	ENSPPYG00000006030	1 retrocopy	retro_pabe_3712,
Pan troglodytes	ENSPTRG00000030691	1 retrocopy	retro_ptro_3176,
Rattus norvegicus	ENSRNOG00000012314	3 retrocopies	retro_rnor_1670, retro_rnor_749, retro_rnor_923,
Sus scrofa	ENSSSCG00000028167	5 retrocopies	retro_sscr_344, retro_sscr_345, retro_sscr_383, retro_sscr_384, retro_sscr_820 ,
Tupaia belangeri	ENSTBEG00000013979	2 retrocopies	retro_tbel_1146, retro_tbel_3713,
Vicugna pacos	ENSVPAG00000001781	2 retrocopies	retro_vpac_398, retro_vpac_418,