RetrogeneDB ID: retro_sscr_68

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:40083095..40084505(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000009866
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000021941
• Aliases: LOC100518654, ZNF3
• Description: None

Sequence

>retro_sscr_68
ATGATGACCAAGGTCCTGGGCATGGCCACGGTCCTGGGCCCGACGCCGCCACAGGAACAGGGGCCCGTGATTGTGAAAGT
CGAGGAGGAAGAGAAAGGGAAGCGCTTGGAGATGTTCCGCCAGCGCTTCAGGCAGTTCGGGTACCATGACACACCTGGGC
CCCGGGAGGCCCTCAGCCAGCTCCGGGTGCTCTGCTGTGAGTGGCTGAGGCCCGAGATCCACACCAAGGAGCAGATCCTG
GAGCTGCTGGTGCTGGAGCAGTTCCTGACCATCCTGCCCCAGGAGCTCCAGGCCTGGGTGCAGGAGCACTGCCCAGAGAG
TGCTGAAGAGGCCGTCACTCTCCTGGAAGATCTGGAGCGAGAACTGGATGAACCAGCACAGCAGGCCTCACCGCCTCCGC
GTGAACAGAGCCAGTCGTGGGAGACGATGTCCTCAGGAACGACCAAGGAGTCCCTGAGCAGCCCGCAGCCCCAGGCTCTG
AAGACCGGGCACCAGTACGAGTCTTGGGGGCCCCTCTACATCCAAGAGACTGGCGAGGAGCAGGGTTTCACGCCAGAGCT
AAGAAAGATTCAAGATCATAAATCGAACACCCAGCATGAGGAAACAACAGATAAGCAGGAAGGTTCTAAAGAATCTCATG
CAGAAGAATTCAGAAGGGATACTGTTCCCATGATTATTGCCAGTAAATGTGAGGCCAGGTTAGAAAGGCAGAGAGTAAAC
CTTGAAAAGGAAAGAGGAACAAAAACCCCTCTCCAAGGCAAAGGTTCCCCCAAACGTAGGGAGTTAATTACTAAACCTGC
CCCAGGAGAGAGACGTTACATATGTGCTGAGTGTGGGAAAGCCTTTAGTAATAGCTCCAATCTCACCAAACACCGGAGAA
CACACACTGGGGAGAAACCGTACGTGTGCACCAAGTGTGGGAAAGCTTTCAGCCACAGCTCAAACCTGACCCTTCACTAC
CGAACACACTTGGTGGACCGGCCCTACGACTGCAAGTGCGGAAAAGCCTTCGGTCAGAGCTCAGACCTCCTGAAACATCA
GCGCATGCACACCGAAGAGGCCCCTTATCAGTGTAAAGATTGCGGAAAAGCCTTCAGCGGCAAAGGCAGCCTCATTCGAC
ACTATCGAATACACACTGGAGAGAAGCCGTATCAGTGTAACGAGTGTGGGAAGAGCTTTAGTCAGCATGCAGGTCTGAGC
TCCCACCAGAGACTCCACACGGGAGAGAAACCATATAAATGTACGGAGTGTGGGAAAGCCTTCAACCACAGCTCAAATTT
TAATAAACACCACAGAATCCACACTGGGGAAAAGCCCTACTGGTGTAGTAATTGTGGGAAAACCTTCTGTAGTAAGTCCA
ACCTCTCCAAACATCAGAGGGTCCACACGGCAGAGAGAGAAGGGCCTTAG

Alignment

ORF - retro_sscr_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMTKVLGMATVLGPRPPQEQGPVIVKVEEEEKGKRLEMFRQRFRQFGYHDTPGPREALSQLRVLCCEWLR
          MMTKVLGMATVLGP.PPQEQGPVIVKVEEEEKGKRLEMFRQRFRQFGYHDTPGPREALSQLRVLCCEWLR
Retrocopy MMTKVLGMATVLGPTPPQEQGPVIVKVEEEEKGKRLEMFRQRFRQFGYHDTPGPREALSQLRVLCCEWLR

Parental  PEIHTKEQILELLVLEQFLTILPQELQAWVQEHCPESAEEAVTLLEDLERELDEPAQQASPPPREQSQSW
          PEIHTKEQILELLVLEQFLTILPQELQAWVQEHCPESAEEAVTLLEDLERELDEPAQQASPPPREQSQSW
Retrocopy PEIHTKEQILELLVLEQFLTILPQELQAWVQEHCPESAEEAVTLLEDLERELDEPAQQASPPPREQSQSW

Parental  ETMSSGMTKESLSSPQPQALETGHQYESWGPLYIQETGEEQGFTPELRKIQDHKSNTQHEETTDKQEGSK
          ETMSSG.TKESLSSPQPQAL.TGHQYESWGPLYIQETGEEQGFTPELRKIQDHKSNTQHEETTDKQEGSK
Retrocopy ETMSSGTTKESLSSPQPQALKTGHQYESWGPLYIQETGEEQGFTPELRKIQDHKSNTQHEETTDKQEGSK

Parental  ESHAEEFRRDTVPMIIASKCEARLERQRVNLEKERGTKTPLQGKGSPKRRELITKPAPGERRYICAECGK
          ESHAEEFRRDTVPMIIASKCEARLERQRVNLEKERGTKTPLQGKGSPKRRELITKPAPGERRYICAECGK
Retrocopy ESHAEEFRRDTVPMIIASKCEARLERQRVNLEKERGTKTPLQGKGSPKRRELITKPAPGERRYICAECGK

Parental  AFSNSSNLTKHRRTHTGEKPYVCTKCGKAFSHSSNLTLHYRTHLVDRPYDCKCGKAFGQSSDLLKHQRMH
          AFSNSSNLTKHRRTHTGEKPYVCTKCGKAFSHSSNLTLHYRTHLVDRPYDCKCGKAFGQSSDLLKHQRMH
Retrocopy AFSNSSNLTKHRRTHTGEKPYVCTKCGKAFSHSSNLTLHYRTHLVDRPYDCKCGKAFGQSSDLLKHQRMH

Parental  TEEAPYQCKDCGKAFSGKGSLIRHYRIHTGEKPYQCNECGKSFSQHAGLSSHQRLHTGEKPYKCTECGKA
          TEEAPYQCKDCGKAFSGKGSLIRHYRIHTGEKPYQCNECGKSFSQHAGLSSHQRLHTGEKPYKCTECGKA
Retrocopy TEEAPYQCKDCGKAFSGKGSLIRHYRIHTGEKPYQCNECGKSFSQHAGLSSHQRLHTGEKPYKCTECGKA

Parental  FNHSSNFNKHHRIHTGEKPYWCSNCGKTFCSKSNLSKHQRVHTAEREGP
          FNHSSNFNKHHRIHTGEKPYWCSNCGKTFCSKSNLSKHQRVHTAEREGP
Retrocopy FNHSSNFNKHHRIHTGEKPYWCSNCGKTFCSKSNLSKHQRVHTAEREGP

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	0.13 RPM	0.13 RPM
SRP014902_testis	1.56 RPM	7.36 RPM
SRP018288_heart	0.42 RPM	2.38 RPM
SRP018288_kidney	0.59 RPM	3.84 RPM
SRP018288_liver	0.00 RPM	3.04 RPM
SRP018288_lung	0.61 RPM	2.85 RPM
SRP018856_adipose	0.11 RPM	1.26 RPM
SRP035408_brain	1.18 RPM	5.65 RPM
SRP035408_liver	0.53 RPM	2.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_68 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_68 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016311	1 retrocopy	retro_ogar_705,
Sus scrofa	ENSSSCG00000021941	1 retrocopy	retro_sscr_68 ,