RetrogeneDB ID: retro_sscr_473

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:124684708..124685456(+)
• Located in intron of: ENSSSCG00000022830

Retrocopy information

• Ensembl ID: ENSSSCG00000016155
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM106C
• Ensembl ID: ENSSSCG00000028397
• Aliases: None
• Description: None

Sequence

>retro_sscr_473
ATGGGATCCCAGCATTCTGCTTCTGCTCACCCCCCTTCCTTCAAGCAAAGGAAAGCAGATGACAGAGAGGACTTGCTGGC
CGAAGGGGAGCAGGAAGAAGCCATTGCTCAGTTCCCATATGTGGAGTTCACCGGGAGAGATAGGCATCAACTGTCTCACT
TGCCAGGGGACAGGCTACATTCCAACAGAGCAAGTAAATGCGTTGGTGGCTTTGAGCCCACACAGTGATCAGAGATTGCG
TCCTCAGAGAACTAAGCAATATGTCCTCTTGTCTGTCCCGCTCTGTCTCCTAGCATCTGGTTTGGTAGTTTTCTTCATAT
TTCCACATTCGGTCCTCATGGATGATGATGGCATCAGAGTGGTGAAAGTAATGTTTAATAAGCAGGAATCCCTTGTAATC
CTCTCCATCCTGGCCACCCTGAAAATCAGAAACTCCAACTTCTATCCAGTGGCGGTGACCAGCCTATCCTGCCAGGTTCA
GTACATGAACACTGTGGTCAAGTCATACATGACCACTAACGTCTCCCTCATTCCACCACAGAGTGCACACCTGGTGAATT
TTACCACAAAGGCTGAAATGGGAGGACCATTTTCCTATATGTATTTCTTCTGCACATTACCCGACATCCTGGTGCACAAT
ATAGTGGTCTTCATGCGGACTTCAGTGAAGATTTCCTACATTGGCCACATGATCCAGAGCTCCTTGGAGACACATCACTA
TGTGGATTGTGGAGCCAATTCCACGGCT

Alignment

ORF - retro_sscr_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 95.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSQHSAFAHPPSCKRRKADDRENFLAEREQEEAIAQFPYVEFTGRD-SITCLTCQGTGYIPTEQVNELV
          MGSQHSA.AHPPS.K.RKADDRE..LAE.EQEEAIAQFPYVEFTGRD..I.CLTCQGTGYIPTEQVN.LV
Retrocopy MGSQHSASAHPPSFKQRKADDREDLLAEGEQEEAIAQFPYVEFTGRD>GINCLTCQGTGYIPTEQVNALV

Parental  ALIPHSDQRLRPQRTKQYVLLSVLLCLLASGLVVFFLFPHSVLVDDDGIKVVKVTFNKQDSLVILAITAT
          AL.PHSDQRLRPQRTKQYVLLSV.LCLLASGLVVFF.FPHSVL.DDDGI.VVKV.FNKQ.SLVIL.I.AT
Retrocopy ALSPHSDQRLRPQRTKQYVLLSVPLCLLASGLVVFFIFPHSVLMDDDGIRVVKVMFNKQESLVILSILAT

Parental  LKIRNSNFYPVAVTSLSSQVQYMNTVVGSYLTSNVSLIPPRSEHLVNFTAKAEMGGPFSYVYFFCTLPDI
          LKIRNSNFYPVAVTSLS.QVQYMNTVV.SY.T.NVSLIPP.S.HLVNFT.KAEMGGPFSY.YFFCTLPDI
Retrocopy LKIRNSNFYPVAVTSLSCQVQYMNTVVKSYMTTNVSLIPPQSAHLVNFTTKAEMGGPFSYMYFFCTLPDI

Parental  LVHNIVVFMRVTANDSYIGHMTQSSLETHHYVDCGANSTA
          LVHNIVVFMR.....SYIGHM.QSSLETHHYVDCGANSTA
Retrocopy LVHNIVVFMRTSVKISYIGHMIQSSLETHHYVDCGANSTA

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	0.14 RPM	29.99 RPM
SRP018288_heart	0.00 RPM	6.89 RPM
SRP018288_kidney	0.39 RPM	27.09 RPM
SRP018288_liver	0.00 RPM	5.76 RPM
SRP018288_lung	0.00 RPM	11.20 RPM
SRP018856_adipose	0.00 RPM	25.46 RPM
SRP035408_brain	0.00 RPM	2.25 RPM
SRP035408_liver	0.00 RPM	4.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_473 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008335	1 retrocopy	retro_cpor_1124,
Equus caballus	ENSECAG00000020351	1 retrocopy	retro_ecab_660,
Echinops telfairi	ENSETEG00000010370	1 retrocopy	retro_etel_173,
Myotis lucifugus	ENSMLUG00000017734	1 retrocopy	retro_mluc_1096,
Pteropus vampyrus	ENSPVAG00000014352	1 retrocopy	retro_pvam_562,
Sus scrofa	ENSSSCG00000028397	1 retrocopy	retro_sscr_473 ,
Tarsius syrichta	ENSTSYG00000001184	1 retrocopy	retro_tsyr_1263,