RetrogeneDB ID: retro_sscr_917

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:112079930..112080611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAK16
• Ensembl ID: ENSSSCG00000015832
• Aliases: None
• Description: MAK16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:13703]

Sequence

>retro_sscr_917
ATACAGTCAGATGATGTTATCTGGAATACACTAGGAAACAACCAAGTTTGTTCCTTCAAAATAAGAACCAAGATTCAGAG
TATTTGCAGAAATAAATATAGCCTGACTGGGCTATGTAATTGGTCATCCTATCCTCTGGCAAATAGTCAATATACCACTA
TCAAAAAAGAGAAAGGGCAGTGCTACTTGTATATAAAAGTTATAGAAGGAGCAGCTTTCCCTAGGCACTTTTGAGAGCAG
GTTTGGCTTCATAAAAATTATGAAAAAGCACTGGAGCAAACAGATAAAAACCTAACTTACTGGCCCCATTTCACTCAACA
CAAATGTAAGCAGAGATTCACCAAGGTCACCCAATATCTAACTCGAATTCGAAAACTTACACTAAAGTGACAGAGGAAAC
TTGTTCCTTTGAGTAAGAAGGTGGAGTGGGAAGGGGAAAAAAAGCAGAGAGGAAAAGGCATTAAGAGCTGCTCAGCTGGA
CAATGTCATGGACAAGAAATGGCTGGAGAGACTGAAACAAGATCAGTATGGCGACATCTACAGCTTTCACATCCATGTCT
TGGACAAGCCGCTGGAAGAGCAGGAGGCAGAGAGTGACTCTTCGGATGCTGAGGAAAAAGATGATGAATAAAATGTGGGA
AGAAGAGAGCTGTGTAAGATGATGATGTGGATGAGAGGGAC

Alignment

ORF - retro_sscr_917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 76.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQSDDVIWDTLGNKQFCSFKIRTKTQSFCRNEYSLTGLCNRSSCPLANSQYATIKEEKGQCYLYMKVIER
          .QSDDVIW.TLGN.Q.CSFKIRTK.QS.CRN.YSLTGLCN.SS.PLANSQY.TIK.EKGQCYLY.KVIE.
Retrocopy IQSDDVIWNTLGNNQVCSFKIRTKIQSICRNKYSLTGLCNWSSYPLANSQYTTIKKEKGQCYLYIKVIEG

Parental  AAFPRRLWERVRLHKNYEKALEQIDENLIYWPRFIRHKCKQRFTKITQYLIRIRKLTLKRQRKLVPLSKK
          AAFPR...E.V.LHKNYEKALEQ.D.NL.YWP.F..HKCKQRFTK.TQYL.RIRKLTLK.QRKLVPLSKK
Retrocopy AAFPRHF*EQVWLHKNYEKALEQTDKNLTYWPHFTQHKCKQRFTKVTQYLTRIRKLTLK*QRKLVPLSKK

Parental  VE-RREKR-REEKALIAAQLDNAIEKELLERLKQDTYGDIYNFPIHAFDKALEQQEAGSDSSDAEEKDEE
          VE...EK..REEKAL.AAQLDN...K..LERLKQD.YGDIY.F.IH..DK.LE.QEA.SDSSDAEEKD..
Retrocopy VEWEGEKK>REEKALRAAQLDNVMDKKWLERLKQDQYGDIYSFHIHVLDKPLEEQEAESDSSDAEEKD--

Parental  DEEDVGKREF-VEDDEVDESD
          DE..VG.RE..V.DD.VDE.D
Retrocopy DE*NVGRREL<V*DDDVDERD

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	7.43 RPM
SRP014902_testis	0.00 RPM	15.56 RPM
SRP018288_heart	0.00 RPM	30.25 RPM
SRP018288_kidney	0.00 RPM	26.79 RPM
SRP018288_liver	0.00 RPM	18.23 RPM
SRP018288_lung	0.00 RPM	30.45 RPM
SRP018856_adipose	0.00 RPM	15.70 RPM
SRP035408_brain	0.00 RPM	19.63 RPM
SRP035408_liver	0.00 RPM	16.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_917 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_917 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009081	5 retrocopies	retro_chof_2336, retro_chof_2538, retro_chof_531, retro_chof_867, retro_chof_948,
Dasypus novemcinctus	ENSDNOG00000008424	1 retrocopy	retro_dnov_624,
Latimeria chalumnae	ENSLACG00000018758	1 retrocopy	retro_lcha_67,
Macropus eugenii	ENSMEUG00000006945	1 retrocopy	retro_meug_1291,
Myotis lucifugus	ENSMLUG00000002758	1 retrocopy	retro_mluc_590,
Oryctolagus cuniculus	ENSOCUG00000008735	3 retrocopies	retro_ocun_1053, retro_ocun_1298, retro_ocun_908,
Sus scrofa	ENSSSCG00000015832	1 retrocopy	retro_sscr_917 ,