RetrogeneDB ID: retro_sscr_798

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:48350426..48351125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS7
• Ensembl ID: ENSSSCG00000012767
• Aliases: None
• Description: HAUS augmin-like complex, subunit 7 [Source:HGNC Symbol;Acc:32979]

Sequence

>retro_sscr_798
ATGGCCGGATTAGTTGCTGTTGGTGAAGGTGGTAGCAGCAAGAATGAGGGCGATGAGGCCGTGTTCAAGGCAGCCATGAA
GGGCTTTGGGAAGCTGAAGGACCTCAATGGTCCCTTCCTCAAGGGTCTTTATATCACCGAACCAAAGACCATTCAGGAAC
TGCTGTGTAGCCCGTCCAAGTACTGTCTGGAAATCCTGGAGTGGATCTGTATCTGTATCTGTCCCTCCTGGCAGGAAAAG
TCCAGCTTGCTGAAGGGGGCCTCAGTGATGGTGATGGTGAAACTAGGCCATAAGCTAATATTGTGTGGGCCTGGTGACTA
GGAGCTCCTGAAGGGCCAGGCCTGCACCCAGAAGCAGCTGTGCTTCATGGACCGATGGCTGGATGTGGTCTGGGACCTGA
TCGTCAGATGCCCCAGCTGCTCCAGCACGAAGGAGTACCTAGAGGCCATCAGGGAGAAGAATGTGGCACTGCTGGGGAGC
TCCTCTTGAGTCCTGACCTGCAGACGTTCCTGAGCCCGGACTGTGACCTGGAGCCCCTGGACACGCAGCCTCTTCTGGAC
AAGCAGGGTGATGACTGGCAGAGCACCAGCCTCGCTGTCCAGTCAGAAGAGAAGGTTCGGAGCTGGCCCCGGGCAGCTGT
AGGAGAGCGCCTTGAAGCTCCAGGTGCTCAGGATGGAGCACAAGCAAGGGGCCACTGTG

Alignment

ORF - retro_sscr_798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 65.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGRVAVGGGGGSEDEGDDAVFKAAVEVFGKLKDLNCPFLEGLYIAEPKTIQELLCSPSKYRLEILEWIC
          MAG.VAVG.GG.S..EGD.AVFKAA...FGKLKDLN.PFL.GLYI.EPKTIQELLCSPSKY.LEILEWIC
Retrocopy MAGLVAVGEGGSSKNEGDEAVFKAAMKGFGKLKDLNGPFLKGLYITEPKTIQELLCSPSKYCLEILEWIC

Parental  IRACPSWQDKVSSLKGASAEAKVQEMVKLGHELMLCGPGDQELLKGRACAQKQLRFMDQLLDVVRSLTVG
          I..CPSWQ.K.S.LKGAS....V..MVKLGH.L.LCGPGD.ELLKG.AC.QKQL.FMD..LDVV..L.V.
Retrocopy ICICPSWQEKSSLLKGAS----VMVMVKLGHKLILCGPGD*ELLKGQACTQKQLCFMDRWLDVVWDLIVR

Parental  CSSGSSTKEHLEDIREKNEALL-GELFLSPHLQTLLSPDCDPGPLDVQPLLDKPRGDRRSTSPSVELEEE
          C.S.SSTKE.LE.IREKN.ALL.GEL.LSP.LQT.LSPDCD..PLD.QPLLDK...D..STS..V...EE
Retrocopy CPSCSSTKEYLEAIREKNVALL<GELLLSPDLQTFLSPDCDLEPLDTQPLLDKQGDDWQSTSLAVQ-SEE

Parental  KVAELAR-QLQESTSKLQALRTEHKPGAAV
          KV....R.QL.ES..KLQ.LR.EHK.GA.V
Retrocopy KVRSWPR>QL*ESALKLQVLRMEHKQGATV

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	10.35 RPM
SRP014902_testis	0.00 RPM	10.33 RPM
SRP018288_heart	0.00 RPM	1.31 RPM
SRP018288_kidney	0.00 RPM	4.83 RPM
SRP018288_liver	0.00 RPM	1.60 RPM
SRP018288_lung	0.00 RPM	8.15 RPM
SRP018856_adipose	0.11 RPM	3.09 RPM
SRP035408_brain	0.00 RPM	2.22 RPM
SRP035408_liver	0.00 RPM	2.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_798 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_798 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000012767	1 retrocopy	retro_sscr_798 ,