RetrogeneDB ID: retro_sscr_88

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:25345681..25347496(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006388
• Aliases: None
• Description: Sus scrofa DDB1 and CUL4 associated factor 8 (DCAF8), mRNA. [Source:RefSeq mRNA;Acc:NM_001244434]

Sequence

>retro_sscr_88
ATGGCTGACGATGAAAGCAGCACAGATGGACCACCAGACTTAGAGAACAGAGGCCTGTCCGATCACCCTGAGGAGAGTTC
TGGAGTGGAGGCAGGGAGGGAGGCCTGCCCCGATACTGAAATTATCTTGAGCGTGACCAGAGGTGGTGGCGATTTTGGCA
GTGGTGGTATTCCCGAACATGCCAGCACAGAAAATCAGGGCACCAGCTCAGAAAGGTCAAGTGAAGACATCGACATTGAA
TGCGTGGAAGATGCTGACAATTTCTTTATCAATGATGAAAACCAGTTCCATTACCGAGAGGAAGAAGAGCTTAGAGAGGA
AGAAGAGTTCGGAGAGGAAGAGCAGGAAGAATTGGCAGAAGAGCAACCTCAGGTACAGTGTGGTGAGGCAAACCATGGTG
AGTGTTTATCAGCTGAGGATCAGGCCCTGGAGGAATGGGTGTCTTCAGAGACATCTGCCCTACCCCTTCCTCGCTGGCGG
GTCCTTAATGCTCTGCGAGAACGGCAGCTGGGTTCAAGTGCCCGCTTTGTGTATGAGGCCTGCGGGGCAAGAGTCTTTGT
GCAGCATTTCCAGTTGCAGTATGGGCTTGAGGGCCACAATGGTTGTGTCAATACTCTGCACTTTAACCAGCGTGGCACCT
GGCTGGCCACAAGCAGTGATGATCTTAAAGTAATATTGTGGGACTGGGTGCGTCAGCAGCCAGTACTGGTCTTTGAGAGT
GGCCACAGAAATAATGTTTTTCAGGCCAAGTTCCTTCCCAACTGTGGTGATCCCACCATGGCCATGTGTGCCCGTGATGG
GCAGGTACGCGTAGCAGAGTTGTCTGCTATACCACACTGCAAGAACACCAAGCGGGTGGCCCAGCACAGGGGAGCCGCCC
ACAAGTTAGCTCTGGAGCCTGACTCCCCTTTTAAGTTCCTAACTTCAGGGGAAGATGCAGTTGTCTTTGCCATTGACCTT
AGACAAGGCCGGCCGGCTTCAAGAGTGGTGGTAACAAAAGATAAGGAGAAGAAAGTGGGACTGTATACAGTCTGTGTGAA
TCCTGCCGATACTTACCAATTTGCAGTGGGTGGACGAGATCAGTTTGTCAGAATTTATGACCAGAGGAAAATTGATGAGA
ATGAGAATAATGGAGTACTCAAGAAATTTTGTCCTCATCACCTGGTCAGCTGTGATTCTACAGCTAACATCACTGGCCTT
GTGTACAGTCACGATGGCACAGAGCTCCTGGCTAGTTACAATGATGAAGATATTTACCTCTTCAACTCTTCTCACTGTGA
TGGTGCCCAGTATGTTAAAAGATACAAGGGACACAGGAATAATGCCACAGTCAAAGGTGTCAATTTCTATGGCCCCAGAA
GTGAGTTTGTCGTGAGCGGTAGTGATTGTGGGCACATCTTTCTCTGGGAGAAATCATCCTGCCAGATTGTTCAGTTCATG
GAGGGAGATAAAGGAGGGACTGTAAACTGTCTTGAGCCCCATCCTTACCTACCTGTGATGGCGACCAGTGGTCTAGACCA
TGATGCTAAGATCTGGGCACCCACAGCTAAAACGACCACTGGCCTTATTGGCTTAAAGAATGTGATTAAGAAGAACAAGC
AGGAACGAGATGAAGATAGCCTGCACCACATTGACCTGTTCGACAGTCACATGCTTAGGTTCCTCATGCATCATCTGACA
CAGAGAGGCCATCACCAGCACTGGCGAAGTCCTGAAGTTGGGGTTATGGATGCAGACTTGGATGAGTCTTCCAGTACCTC
AGATACATCAGAGGAGGAAGACAACCAAGACGAAATGCAGTGCCTGCCATCCTGA

Alignment

ORF - retro_sscr_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 90.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSTESRGTDTE-SSGEDKDSDSMEDTGHYSINDENQVHDPSEEEEEEEEE-EEEHPRRRVQRKRANRDQD
          TS.E....D......ED.D.....D........E.......E..EEE.EE..EE.P...VQ...AN....
Retrocopy TSSERSSEDIDIECVEDADNFFINDENQFHYREEEELREEEEFGEEEQEELAEEQPQ--VQCGEANHGEC

Parental  SSDDERALEDWVASETSALPRPRWQALPALRERELGSSARFVYEACGARVFVQRFRLQHGLEGHTGCVNT
          .S....ALE.WV.SETSALP.PRW..L.ALRER.LGSSARFVYEACGARVFVQ.F.LQ.GLEGH.GCVNT
Retrocopy LSAEDQALEEWVSSETSALPLPRWRVLNALRERQLGSSARFVYEACGARVFVQHFQLQYGLEGHNGCVNT

Parental  LHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQAKFLPNSGDSTLAMCARDGQVRVAELS
          LHFNQRGTWLA..SDDLKV..WDWVR.QPVL.FESGH..NVFQAKFLPN.GD.T.AMCARDGQVRVAELS
Retrocopy LHFNQRGTWLATSSDDLKVILWDWVRQQPVLVFESGHRNNVFQAKFLPNCGDPTMAMCARDGQVRVAELS

Parental  ATQCCKNTKRVAQHKGASHKLALEPDSPCTFLSAGEDAVVFTIDLRQDRPASKLVVTKEKEKKVGLYTIY
          A...CKNTKRVAQH.GA.HKLALEPDSP..FL..GEDAVVF.IDLRQ.RPAS..VVTK.KEKKVGLYT..
Retrocopy AIPHCKNTKRVAQHRGAAHKLALEPDSPFKFLTSGEDAVVFAIDLRQGRPASRVVVTKDKEKKVGLYTVC

Parental  VNPANTHQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLVNSESKANITCLVYSHDGTELLASYND
          VNPA.T.QFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLV...S.ANIT.LVYSHDGTELLASYND
Retrocopy VNPADTYQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLVSCDSTANITGLVYSHDGTELLASYND

Parental  EDIYLFNSSHSDGAQYIKRYKGHRNNATVKGVNFYGPKSEFVVSGSDCGHIFLWEKSSCQIIQFMEGDKG
          EDIYLFNSSH.DGAQY.KRYKGHRNNATVKGVNFYGP.SEFVVSGSDCGHIFLWEKSSCQI.QFMEGDKG
Retrocopy EDIYLFNSSHCDGAQYVKRYKGHRNNATVKGVNFYGPRSEFVVSGSDCGHIFLWEKSSCQIVQFMEGDKG

Parental  GVVNCLEPHPHLPVLATSGLDHDVKIWAPTAETSTELTGLKDVIKKNKRERDEDSLHHTDLFDSHMLWFL
          G.VNCLEPHP.LPV.ATSGLDHD.KIWAPTA.T.T.L.GLK.VIKKNK.ERDEDSLHH.DLFDSHML.FL
Retrocopy GTVNCLEPHPYLPVMATSGLDHDAKIWAPTAKTTTGLIGLKNVIKKNKQERDEDSLHHIDLFDSHMLRFL

Parental  MHHLRQRRHHRRWREPGVGATDADSDESPSSSDTSDEEEGPDRVQCMPS
          MHHL.QR.HH..WR.P.VG..DAD.DES.S.SDTS.EE...D..QC.PS
Retrocopy MHHLTQRGHHQHWRSPEVGVMDADLDESSSTSDTSEEEDNQDEMQCLPS

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	39.69 RPM
SRP014902_testis	0.85 RPM	122.63 RPM
SRP018288_heart	0.00 RPM	105.69 RPM
SRP018288_kidney	0.00 RPM	143.62 RPM
SRP018288_liver	0.00 RPM	71.96 RPM
SRP018288_lung	0.00 RPM	108.65 RPM
SRP018856_adipose	0.14 RPM	130.19 RPM
SRP035408_brain	0.00 RPM	56.95 RPM
SRP035408_liver	0.00 RPM	60.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_88 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_88 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88 ,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,