RetrogeneDB ID: retro_sscr_971

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:70073096..70073539(+)
• Located in intron of: ENSSSCG00000008927

Retrocopy information

• Ensembl ID: ENSSSCG00000008928
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSSSCG00000000635
• Aliases: None
• Description: mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]

Sequence

>retro_sscr_971
ATGTCTATAGCCAGCGATTTCTACCTGCACTACTACATAGGACACAAGGGCAAGTTTGGACACGAGTTTCTGGAGTTCGA
GTTTCAGCCGGACGGAAAACTTAGATATGCCAACAACAGCAATTATAAAAATGATGTCATGATCAGAAAGGAGGCTTATG
TACACAAGAGTGTAATGGAAGAACTGAAGAGAATTATTGATGACAGTGAAATTACAAAGGAAGATGATGCTTTGTGGCCT
CCTCCTGACAGGGTTGGTCGGCAGGAGCTTGAAATTGTGGTTGGAGATGAACACATTTCTTTCACCACATCAAAAATAGG
TTCTCTTATTGATGTTAATCAGTCAAAGGATCCTGAAGGCCTTCGAGTATTTTATTATTTGGTACAGGACCTGAAATGTT
TAGTTTTTAGTCTATTGGATTACATTTCAAGATTAATCCAATC

Alignment

ORF - retro_sscr_971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
          MS.ASDFYL.YY.GHKGKFGHEFLEFEF.PDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
Retrocopy MSIASDFYLHYYIGHKGKFGHEFLEFEFQPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE

Parental  ITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSL-I
          ITKEDDALWPPPDRVGRQELEIV.GDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSL.I
Retrocopy ITKEDDALWPPPDRVGRQELEIVVGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSL<I

Parental  GLHFKIKPI
          GLHFKI.PI
Retrocopy GLHFKINPI

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	2.79 RPM
SRP014902_testis	0.00 RPM	11.88 RPM
SRP018288_heart	0.00 RPM	4.66 RPM
SRP018288_kidney	0.10 RPM	8.67 RPM
SRP018288_liver	0.00 RPM	8.95 RPM
SRP018288_lung	0.00 RPM	8.55 RPM
SRP018856_adipose	0.02 RPM	11.28 RPM
SRP035408_brain	0.00 RPM	9.05 RPM
SRP035408_liver	0.00 RPM	9.28 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_971 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_971 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019235	1 retrocopy	retro_btau_399,
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Myotis lucifugus	ENSMLUG00000003527	2 retrocopies	retro_mluc_1039, retro_mluc_2484,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Sus scrofa	ENSSSCG00000000635	1 retrocopy	retro_sscr_971 ,
Sus scrofa	ENSSSCG00000003849	3 retrocopies	retro_sscr_1007, retro_sscr_706, retro_sscr_977,
Tursiops truncatus	ENSTTRG00000001272	2 retrocopies	retro_ttru_515, retro_ttru_647,