RetrogeneDB ID: retro_sscr_80

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:87445812..87446970(+)
• Located in intron of: ENSSSCG00000006277

Retrocopy information

• Ensembl ID: ENSSSCG00000006278
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006846
• Aliases: None
• Description: None

Sequence

>retro_sscr_80
AACAAAATGGCAGAAGACAAAGAGTGCCACAGCATGGTTGAAGAGGTTCCCAGCAAAAGGATAATTAAGTTTAATCCTCC
GTTATACAAACAACGTTACCAGTTTGTTAAAAATTTAGTGGAGCAACATCAGCCTCAAAAGGTTGCAGACCTAGGGTGTG
GTGATCTTTCGCTCCTATCGATATTAAAATACCTAAAGTGTGTCACAGAGCTTGTCGGAGTAGACATCAATGAAGGCAGA
CTTAAATGGAATGGGTCTCGGCTGTCCCCATGTGTGGGGGACCATCTGGATCCCCGCGAGCTGGATTTAGTCATTACCTT
GTATCATGGCTCTGTTTTGGAGAAAGACTGTCGTTTGCTCGGATTTGACTTGGTAACATGTATTGAACTAATAGAACATT
TTGATTCAGAAGATCTGGCCAGGTTTCCCGAAGTTGTTTTTGGGTACATGTCTCCAGCCATGATTGTCATCAGCACACCG
AACTCTGATTTCAATTCCCTGTTTCCGCTCTCAGTCTTCAGAGATTCAGATCACAAATTTGAGTGGAGTAGAGTGCAGTT
TCAGACCTGGGCTTTAGATGTGGCAAATCGCTATAGCTACTCAGTGGAGTTCACCGGTGTAGGGGAACCGCCGGCAGAAG
CTGAGGATGTTGGATATTGTACCCAGATAGGGGTCTTCCGGAAGAAAGAAAAGACAACTGAATCTGATGTTTTGGAGCAC
CCTGGCGAACGTGTTTATGAAGTTGTTTATACGACCTCATACCCAAGTTTACAGCAAATAAATTACCATAGACGTGTTGT
GGTTTATCTGGTATACCGAGAAGTGAACAAAATGAGACTGAGATACCAAGTGAGTCTGAGGCGGCACGAACTGGAACCTG
AGTCCACAGACCCTGACGACCCCAGAAGAAAATTCATCTCAGGCCTTCCAGTTCATACACCCACAGAAGCTGACAAAGCC
ATGGCGATGACTCCCCAACCTTTCTGTATTGGAGATAAGTTTTACGTACCCCTGAAAAGAATCATTGCTTATCCCAGGCT
GGGGTACTTATGTGGTAATGTGCAGGAGCTGAGAGAGCTCCTCGCGGACTCAATAGAACTGAACTGTGATGCGTCTGCGG
TGAAGGTTGACTTGTATCACTGTAGTGACTACTGCTGA

Alignment

ORF - retro_sscr_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.2 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QCHSVVEEVPSKRIIKFNPPLYKQRYQFVKNLVEQHQPQKVADLGCGDLSLLSILKYLKCVTELVGVDIN
          .CHS.VEEVPSKRIIKFNPPLYKQRYQFVKNLVEQHQPQKVADLGCGDLSLLSILKYLKCVTELVGVDIN
Retrocopy ECHSMVEEVPSKRIIKFNPPLYKQRYQFVKNLVEQHQPQKVADLGCGDLSLLSILKYLKCVTELVGVDIN

Parental  EGRLKWNGSRLSPCVGDHLDPRELDLVITLYHGSVLEKDCRLLGFDLVTCIELIEHFDSEDLARFPEVVF
          EGRLKWNGSRLSPCVGDHLDPRELDLVITLYHGSVLEKDCRLLGFDLVTCIELIEHFDSEDLARFPEVVF
Retrocopy EGRLKWNGSRLSPCVGDHLDPRELDLVITLYHGSVLEKDCRLLGFDLVTCIELIEHFDSEDLARFPEVVF

Parental  GYMSPAMIVISTPNSDFNSLFPLSVFRDSDHKFEWSRVQFQTWALDVANRYSYSVEFTGVGEPPAEAEDV
          GYMSPAMIVISTPNSDFNSLFPLSVFRDSDHKFEWSRVQFQTWALDVANRYSYSVEFTGVGEPPAEAEDV
Retrocopy GYMSPAMIVISTPNSDFNSLFPLSVFRDSDHKFEWSRVQFQTWALDVANRYSYSVEFTGVGEPPAEAEDV

Parental  GYCTQIGVFRKKEKTTESDVLEHPGERVYEVVYTTSYPSLQQINYRRRVVVYLVYREVNKMRLRYQVSLR
          GYCTQIGVFRKKEKTTESDVLEHPGERVYEVVYTTSYPSLQQINY.RRVVVYLVYREVNKMRLRYQVSLR
Retrocopy GYCTQIGVFRKKEKTTESDVLEHPGERVYEVVYTTSYPSLQQINYHRRVVVYLVYREVNKMRLRYQVSLR

Parental  RHELEPESTDPDDPRRKFISGLPVHTPTEADKAMAMTPQPFCIGDKFYVPLKRIIAYPRLGYLCGNVQEL
          RHELEPESTDPDDPRRKFISGLPVHTPTEADKAMAMTPQPFCIGDKFYVPLKRIIAYPRLGYLCGNVQEL
Retrocopy RHELEPESTDPDDPRRKFISGLPVHTPTEADKAMAMTPQPFCIGDKFYVPLKRIIAYPRLGYLCGNVQEL

Parental  RELLADSIELNCDASAVKVDLYHCSDY
          RELLADSIELNCDASAVKVDLYHCSDY
Retrocopy RELLADSIELNCDASAVKVDLYHCSDY

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	1.33 RPM
SRP014902_testis	0.00 RPM	2.97 RPM
SRP018288_heart	0.00 RPM	0.05 RPM
SRP018288_kidney	0.00 RPM	0.79 RPM
SRP018288_liver	0.00 RPM	0.32 RPM
SRP018288_lung	0.00 RPM	0.20 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.16 RPM
SRP035408_liver	0.00 RPM	0.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_80 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_80 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004357	1 retrocopy	retro_amel_532,
Otolemur garnettii	ENSOGAG00000013441	4 retrocopies	retro_ogar_1961, retro_ogar_2013, retro_ogar_2135, retro_ogar_562,
Sus scrofa	ENSSSCG00000006846	1 retrocopy	retro_sscr_80 ,