RetrogeneDB ID: retro_sscr_1183

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:18146422..18146701(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031052
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL13
• Ensembl ID: ENSSSCG00000005996
• Aliases: None
• Description: mitochondrial ribosomal protein L13 [Source:HGNC Symbol;Acc:14278]

Sequence

>retro_sscr_1183
TCATCAACTGACTACCCAGGTGGATTCAGACAAGTAACAGCTGCTCAGCTTCGCCGGAAGGATACAATGGCAATTGTAAA
ACTAGCTGTTTATGGCTTGTTGCCAAAAAACCTTCACAGAACTATGATGCAGAGGTTGCATCTTTTCCCAGATGAAGATA
TACCAGAAGATATCCTTAAGAATTTAGTGGAAGAGTTTCTTTAACCATGAAAAGTGCTCTGACGTCTAGATGAGTACACA
TAAGAAGAAATAGAGGCTTTCCCAAGAGTTTGGTCTCCA

Alignment

ORF - retro_sscr_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHTGYPGGFRQVTAAQLHQKDPVAIVKLAIYGMLPKNLHRRTMMQRLHLFPDEDIPEDILKNLVEELPQP
          S.T.YPGGFRQVTAAQL..KD..AIVKLA.YG.LPKNLH.RTMMQRLHLFPDEDIPEDILKNLVEE...P
Retrocopy SSTDYPGGFRQVTAAQLRRKDTMAIVKLAVYGLLPKNLH-RTMMQRLHLFPDEDIPEDILKNLVEEFL*P

Parental  RKVPRRLDEYTQEEIEAFPRVWSP
          .KV..RLDEYT.EEIEAFPRVWSP
Retrocopy *KVL*RLDEYT*EEIEAFPRVWSP

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	5.57 RPM
SRP014902_testis	0.00 RPM	13.15 RPM
SRP018288_heart	0.00 RPM	17.71 RPM
SRP018288_kidney	0.00 RPM	20.59 RPM
SRP018288_liver	0.00 RPM	12.47 RPM
SRP018288_lung	0.00 RPM	10.59 RPM
SRP018856_adipose	0.00 RPM	11.02 RPM
SRP035408_brain	0.00 RPM	43.42 RPM
SRP035408_liver	0.00 RPM	31.97 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1183 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183 ,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,